I've noticed that I make very little use of subsystem targeting. In fact, on some ships I almost forget I have these abilities.
If I can choose between an overload that will take down most if not all shielding on my target, plus add a chance to deal shield ignoring damage for a few seconds whenever the shields don't go down in one shot on the one hand, and subsystem targeting that may or may not disable a subsystem, I have little reason to choose the latter.
Most sci ships which have access to subsystem targeting don't have that many tactical abilities. Which is another reason why overload or FAW will usually be the more interesting option.
I believe that innate subsystem targeting (not the Boff skills, only the ST that come with a ship itself) would be much more useful if it didn't share its cooldown with overload or FAW.
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http://sto.gamepedia.com/Subsystem_Targeting
The OPs point is why would you bother using this ability (baked in or not) over FaW or BO?
Removing the cooldown with other beam powers may increase SST usefulness/use with players, I would also tweak the ability to allow its use with cannons and make it more likely to strip power altogether or for a longer period.
At the moment it's just a complete waste because any ship can fit (to my knowledge) Bfaw x2.
My 2c.
Because they are different abilities with different intended uses. It is a Debuff and not a Spam. You use it to supplement other Drain Abilities.
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Yet, in a game where DPS is king, the prevailing wisdom would state that using anything other than the DPS granting ability is at best sub-optimal, more appropriately "epic fail of build".
Considering the fact that "baked in SST" is given to science ships partially as an offset to their "missing" weapons slot(s), it should be on a separate cooldown from the BOff beam skills. Even if the "baked in versions" are clones of the actual ensign abilities, and editing one would edit the other - the fact that SST is a debuff while BFaW & BO are damage boosters means they should theoretically be on separate cooldowns anyway (much as GW for DPS and Energy Syphon for drain - both deflector abilities - are on separate cooldowns)...
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It should most definitely be made available to cannons, as even cannons in show were able to be used to attack subsystems!
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An idea I had that Beam Target Subsystem would be an ongoing buff that added some energy drain and disable chance to your beam attacks (maybe actaully it should affect all attacks) for 10-15 seconds. It almost certainly shouldn't work with BFAW then, though, that would make things even worse.
Maybe some Starship Traits or Reputuation Traits could be introduced:
Improved Subsystem Targeting (Starship Trait?)
When you activate Beam Target Subsystems, for 10 seconds all your beam attacks have a 5 % chance to disable the selected subsystem for 5 seconds.
Rapid Subsystem Targeting (Reputation Trait?)
When you activate Beam Target Subsystem, you also gain +33 % weapon haste for all energy weapons for 10 seconds.
Subsystem Targeting Synergy (Reputation Trait?)
When you activate Beam Target Subsystem, your next torpedo attack also has a 15 % chance to disable the selected subsystem for 5 seconds. In addition, your cannon shots drain 2 points of enegy from the selected subsystem per hit for the next 10 seconds.
Coordinated Subsystem Targeting (Starship Trait?)
When you activate a Beam Target Subsystem, all your hangar pets also activate Beam Target Subsystem I.
One thing that does come to mind is that having these sub-system targeting abilities native to the ship, does also mean you do not waste tactical slots on them. Though i can see the merits of not having them share a cannon spread with the other tactical attack abilities like beam overload or bfaw, and then implementing some interactions between these abilities as well as with the cannon versions. Like that using a beam overload/cannon rapid-fire might increase the chance of knocking a system offline an increase the power drain, while using bfaw/cannon spread would give you the ability to hit multiple , but yet since this attack is targeting very specific systems/area of the ship it would reduce the effective strength of your attacks. I mean this is meant to be something used to improve the parties output thru the use of, and is much more like the stereotypical support style of play, which is somewhat lacking right now.
I like the idea and concept of these starship/rep traits, though if you are going to have hanger-pets use things like sub-system targeting, maybe make it more that when you use it with pets out they buff your sub-system target attack's effectiveness. I agree to extent that just making sub-system targeting work with bfaw without some kind of trade-off would be a bad idea, and so maybe make it that while using them both at the same time it would reduce the power drain an chance to knock off-line a sub-system by a certain amount to counter the fact you are able to inflict this on multiple targets or times.