Edit: Someone pointed me to BigBadB's website which is just chock full of great information, and much more detailed than what I have here. I highly recommend that you check it out, here are links to two great articles that go over skills and ship mechanics:
Skills: the numbersStarship Mechanics
B provides much more detail than I did below. The only information from below that isn't already covered is the changes to T3 and T4 ship skills, and I am sure that B will update with that soon.

With the changes to the Captain skills, I thought it might be helpful to provide information relating to the relative benefit provided by each skill. Each skill provides a percentage increase to the hull strength, speed, and turn rate of one or more ships. I will outline each skill as it impacts Tier 5 ships, its cost, percentage increase per rank, and the Return On Investment (ROI) per 100 skill points spent. I will also provide several sample builds and their aggregate benefit and ROI.
Tier 1: Starship Command: costs 100 points per rank. The benefit applies to all ships you may fly (6 different ships at T5), at max rank you receive a total of 18% increase.
Rank ___Benefit___ROI (per 100 skill points spent)
1_______6%______6
2_______4%______4
3_______2%______2
4_______2%______2
5_______1%______1
6_______1%______1
7_______1%______1
8_______0.5%_____.5
9_______0.5%_____.5
Tier 2: Cruiser Captain, Escort Captain, and Science Vessel Captain: costs 200 points per rank. The benefit applies to the class of ships referenced in the name (2 different ships at T5), at max rank you receive a total of 30% increase.
Rank____Benefit___ROI (per 100 skill points spent)
1_______8%______4
2_______6%______3
3_______4%______2
4_______4%______2
5_______2%______1
6_______2%______1
7_______2%______1
8_______1%______.5
9_______1%______.5
Tier 3: Heavy Cruiser Captain, Heavy Escort Captain, and Research Science Vessel Captain: costs 300 points per rank. The benefit applies to the class of ships referenced in the name (2 different ships at T5). Note that full benefit from this skill is only applied to T3 ships of the appropriate class. Only 1/4 of the normal benefits of this skill apply to T5 ships. The numbers provided in this table represent the T5 benefit. At max rank you receive a total of 13% increase.
Rank____Benefit___ROI (per 100 skill points spent)
1_______2.5%_____.83
2_______2%______.67
3_______1.5%_____.5
4_______1.5%_____.5
5_______1.5%_____.5
6_______1%______.33
7_______1%______.33
8_______1%______.33
9_______1%______.33
Tier 4: Exploration Cruiser Captain, Tactical Escort Captain, Long Range Science Vessel: costs 400 points per rank. The benefit applies to the class of ships referenced in the name (2 different ships at T5). Note that full benefit from this skill is only applied to T4 ships of the appropriate class. Only 1/4 of the normal benefits of this skill apply to T5 ships. The numbers provided in this table represent the T5 benefit. At max rank you receive a total of 13% increase.
Rank____Benefit___ROI (per 100 skill points spent)
1_______2.5%_____.63
2_______2%______.5
3_______1.5%_____.38
4_______1.5%_____.38
5_______1.5%_____.38
6_______1%______.25
7_______1%______.25
8_______1%______.25
9_______1%______.25
Tier 5: Assault Cruiser Captain, Star Cruiser Captain, Advanced Escort Captain, Fleet Escort Captain, Deep Space Science Vessel Captain, and Reconnaissance Science Vessel Captain: costs 500 points per rank. The benefit applies only to the specific ship referenced in the name (1 ship at T5). At max rank you receive a total of 52% increase.
Rank____Benefit___ROI (per 100 skill points spent)
1_______10%_____2
2_______8%______1.6
3_______6%______1.2
4_______6%______1.2
5_______6%______1.2
6_______4%______.8
7_______4%______.8
8_______4%______.8
9_______4%______.8
Build examples:
I will outline a few build examples and illustrate their aggregate ROI per 100 skill points. I will list the Tier and number of ranks, total skill point cost, and aggregate ROI. For the benchmark, I will use a popular build for Captain skills prior to the patch.
Benchmark: T1 (9) + T2 (9) + T5 (9) = 7200 points spent, 100% benefit, 1.38 aggregate ROI
Using an ROI target per rank of >= 1 : T1 (7) + T2 (7) + T5 (5) = 4600 pts, 81%, 1.76 ROI
Using an ROI target per rank of >= .75 : T1 (7) + T2 (7) + T3 (1) + T5 (9) = 6900 pts, 99.5%, 1.44 ROI
Using an ROI target per rank of >= .51 : T1 (7) + T2 (7) + T3 (2) + T4 (1) + T5 (9) = 7600 pts, 104%, 1.38 ROI
Using an ROI target per rank of >= .4 : T1 (9) + T2 (9) + T3 (5) + T4 (2) + T5 (9) = 9500 pts, 113.5%, 1.19 ROI
Using an ROI target per rank of >= .25 : T1 (9) + T2 (9) + T3 (9) + T4 (9) + T5 (9) = 13500 pts, 126%, 0.93 ROI
Since Tier 5 skills are at a premium with the current skill cap, here are a few builds with no points in T5. One side benefit of these builds is that the benefit applies to 2 ships in T5 (both escorts, both cruisers, both science vessels, depending).
No T5 skills, with Max %benefit : T1 (9) + T2 (9) + T3 (9) + T4 (9) = 9000 pts, 74%, 0.82 ROI
No T5 skills, target ROI >= .4 : T1 (9) + T2 (9) + T3 (5) + T4 (2) = 5000 pts, 59.5%, 1.19 ROI
No T5 skills, target ROI >= .51 : T1 (7) + T2 (7) + T3 (2) + T4 (1) = 3100 pts, 52%, 1.67 ROI
Comments
What bonus does each maxed out skill gives to a tier 5 vessel and what's is there a difference between the final bonus before the patch and now?
Max Tier 2 = 30% (1800 skill points to max)
Max Tier 3 = 13% (2700 skill points to max)
Max Tier 4 = 13% (3600 skill points to max)
Max Tier 5 = 52% (4500 skill points to max)
Maxed all = 126% total (but note that you have to spend 13,500 skill points to get that max)
Its important to note, though, that you do not get equal "bang for your buck" for each rank purchased.
interesting, so tier 2 gives you a 30% increase and tier 3 and 4 only give you a 26% increase combined.
Maxing out everything except tier 5 gives you a 56% increase to stats.
With the new attack vector skills, I wonder if it would be more beneficial to use those to increase your ships abilities after a certain point rather than maxing out your ship skills at all.
In fact, with those skill maxed, what kinda bonuses would your ship get opposed to upgrading the ship skills themselves I wonder.