Got my first level 50 last night.
Just wanted to say thanks to those that answered my posts on this forum, that helped me along the way.
Of course I now have a couple more questions now I am 50

I have about 45% of the standard "Story" missions left, is it worth doing them or should I just start with the L50 stuff.
Regarding the L50 stuff, where's the best place to start, anything I need to be concentrating on?
Thanks again.
Comments
You probably want to join the crowd doing the multiplayer-stuff that makes most of the 'endgame' content - preferably with good enough skill as a player and gear as to be of actual assistance than a liability.
In regards to gear, I'd like to bring forth this link, which in turn is also an answer to Your question: yes, it can be worthwhile to play and/or repeat Episodes to get specific gear that might make things easier. I also tried giving a bit of advice there but feel free to look for more or ask.
Regarding build, which ship to choose, which Bridge Officer abilities to use and all that - that is quite a lot to summarize and there are countless players who have already done so. I'd start here at the Academy or in the Player Guides section and search.
And beyond that, what else is there to be done - well, You might want to look into the Reputation systems. Every Reputation system can grant You access to more gear and new Traits to select so they quickly become part of a grind. Fear not, they are (mostly) well worth the effort as some of the item sets that can be found in those reputation systems are still among if not the best You can get. You will usually need to do multiplayer missions for them to get the specific kind of Marks You need to fill the reputation projects. Google for the name of those missions in the PvE list and You should manage to find a walkthrough that other players made. Read those. Seriously.
Good luck!
Taskforce 47 Falkenwacht (Federation) / Greifenreiter (KDF)
(at) deianirrah
Free Gear and where to get it
The story missions will give you insight into the story and make some aspects of the "endgame" more understandeable (what's up with the Dyson Spheres, for example).
You may also want to ask around which missions have good gear that you may want to play (possibly even replay) to get the level 50 version of that gear. This can help make Elite PvE a bit easier and, quite possibly also PvP (but I think in PvP, your main problem is the lack of experience in teamwork and dealing with enemies that think and use their (large) suite of abilities effectively.)
some of the story missions are worth doing
For item rewards:
Fluid Dynamics, Borg Mission Chain, doing this 6 times over gives you a solid set of antiproton beam arrays.
All of the Dyson Sphere Chain (these can be run a couple times to get a couple of good items sets and are by far the highest quality story missions in the entire game)
Parts of the Cardassian Struggle (there are 2 missions that you run, and then run one a second time and you now have yet another set)
Parts of the breen arc (for the breen item set)
I would concentrate on the rep system though, Dyson and Borg are easy to level and the item sets you can get from them are some of the best in the game. Borg should be leveled in either Normal level queued missions (infected conduit (space) and khitomer vortex (space) being the best, or elites if you have a pre-made team willing to teach and carry you the first few times.) The Borg Elite missions are worth learning how to do as they reward large amounts of marks and dilithium, as well as MK XI/XII items
you can level dyson through the ground battlezone fairly easily too
As another note: The dyson missions give you an item set with + damage two piece bonus to antiproton, goes well with those antiproton beams
I find when I am playing with buddies from my fleet I am having the most fun. I would search for a fleet that is active and still leveling that way you can contribute to fleet progression. I prefer ones that use team speak or mumble.
I would also Dyson ground battle zone to instances a day for your dilithium.
Here is some channels that will help you and are pretty active that you can join.
NOP public service
Doffcalls
Doffjobs
Publicelitestf
Publicnws
Accolades
Redalert
These channels are active and are willing to help most of the time
If you like to PvP join organizedpvp.
You can get great equipment really useful if you going for specific builds. Since you said you have about 45% of the missions not done yet, you still didnt have the chance to do the dominion episodes, or the breen ones, or the borg ones.. all those episodes grants you really good equpiment, and the jem hadar set is great if you going to use polaron weapons, for example (and forget about maco and reputation sets, but of course you need to pick the lobi mkXII version once you have the mkxi). Or the equipment you get doing the breen episodes, the set is awesome if you use a transphasic torp build, for example. And the equipment you get once you reach the Borg episodes is great, you get a good ground kit, a really good ground armor (better for example than the jem hadar one) and some other things really useful.
Not to mention, some dilithium daily missions are only available when you reach some episodes, for example, you cant do the daily defera missions until you finish the Breen story arc. And the solanae set, that you can adquire after the Borg episodes, is the best free set you will get in the game.
So, yes, you should do the rest of the episodes, it is a must.
What i do when i create a new toon is to reach level 50 before i start the dominion story arc. That way i can get the equipment from those episodes at its max level. This is maybe a stupid advise, but it is a really useful one lol. Because for example, some items are part of a set, and to complete that set you will need em at its max level. So if you are level 40 when you reach the dominion episodes, you will only get MK X versions of em... and you will need to replay that episode again when you are level 50 if you want to gather the mkXI version...
The overhauled Borg/Undine series is really solid too, though we all miss Q.
I am simply having fun playing some of the end game content which I mostly do to gather dilithium ore. My Fed toon is mostly focused on Borg elite STFs (got over 21k Omega Marks) which gives 960 dilithium. I have a much lower emphasis on Voth elite STFs (got around 3k Dyson Marks) since it only rewards 240 dilithium. I am going the reputation systems for both Omega and Dyson. Crystalline Catastrophe elite is another STF that I play pretty often (got around 7k Nukara Marks) since it rewards 960 dilithium, but I am not interested in the Nukara rep system. I play the Azure Nebula Rescue from time to time just for fun; it does not really reward many Romulan Marks and it also does not reward any dilithium... so like I said, I just play that for fun.
If you want to farm dilithium ore, then playing the STFs is a good way to do so especially since 50 marks can be turned in for 500 dilithium ore. Personally, I have not do this yet. "Spotlight" Foundry missions (community created missions) are also a good way to earn dilithium; "Spotlight" are considered to be higher quality community content and rewards between 1,440 - about 3,050 dilithium depending on the length on the average time it takes players to complete the mission. This reward is only given once every 20 hours.
I spend a decent amount of time doing the Doff missions currently trying to max out all my commendations to level 4; only 3 more to go. On top of that I am also slowly increasing the quality of my Doffs; I do not have any more white Doff and I am currently replacing green Doff with either blue or purple Doffs. The ultimate goal is to have all 400 Doff for my Fed toon to be purple and all 300 Doff for my KDF toon to be purple as well.
There is a decent amount of end game content to play, but it can be repetitive. So perhaps you may want to go back and do the story missions and / or create another toon and play both of them for a change of pace.
I am currently leveling up a 3rd toon, Romulan, and it brings a nice perspective into the game. All three factions have certain unique story line missions so it a nice way to experience something different and also see that larger overall picture. However, trying to find time to devote to all 3 toons can be a challenge. In addition, all three toons are of different classes which further adds in a nice bit of change.
My Fed toon is an Engineer and flies cruisers. My KDF toon is Tactical and exclusively flies Birds of Prey (BoPs) even for elite STF missions. My Romulan toon is Science, but unfortunately prior to reaching level 40, Romulan do not really have much choice in terms of free starships. I have been flying Warbirds that are more like cruisers or escorts. I cannot select a science ship until I reach level 40. All three classes as well as different types of ships requires you to develop different strategies for each toon. That is a nice change of pace.
Everything eventually go back to grinding dilithium ore though which gets refined to dilithium crystals which can then be converted to Zen. Combined with spending real money on Zen from time to time I can buy things from the C-Store for my toons like a new starship. However, the Zen I have used so far has been to increase the number of Doff slots for all my toons.
Yeah. The revamped work done in the Borg missions is awesome. I for once need to congrats cryptic for that, i wish they put the same interest and work in everything else.. sigh.
I am a very new Lev 50 and I acquired some decent equipment for my ship which saved me spending Credits.
I also found the last few Dyson missions to be amazing fun ... Very proud of my little ship for pulling me through :-)
Which rep gear should I use for Engineer's Ground and Space sets.
For weapons side. ive collected some 5x XII plasma beams from daily box reward while leveling Romulan rep.
I also just got the new Risa cruiser recently...I've installed the Plasma beams in there but idk which rep gear set upgrade I should aim towards. share your suggestions thanks
I like the Solanae (3 out of 4 set pieces) space set from the Featured Episode "A Step Between Stars." It offers really good survivability, and can help a long way. However you do need to be level 50 to run the mission. Also, it is free, and you don't need the rep system to get it.
If you just want to go with the rep gear, and spend the cost for it, I would recommend taking a look at what your weakness is. Every player has something they rank the lowest in. It is either survivability, damage output, or speed (which can help with survivability).
All of the rep system gear is good for certain builds. If you need survivability, and want a space set from the rep system, the Assimilated space set from the Omega rep system is good. It also offers good speed as well.
If you are interested in the sets, I recommend checking out the STO wiki. You can look at info cards on that site that will show the information of each piece. Also, it sometimes has accurate information on the set piece bonuses. However, keep in mind that the information cards usually have the accurate information, some of the other information is not always as accurate.
It is a good place to do some homework, find sets you might like to pick from, then ask on the forums what others that use(d) them think about them.
Keep in mind though, if you get rep gear just because it is the most popular, it might not help you any. The rep gear can be just like any other gear in the game. For example, if you fly an escort, and it has high turn rate, and you have no problems with it, but someone else using the same ship has trouble flying it, and recommends an RCS console, you just put a console on that will not do you any good.
It is the same with the rep system gear. It should help fill in where you have a weakness, and boost stats that might be lacking.