I understand that, but it's the particular splits you've chosen that seem a little weird, and really mean to destroyers - with one exception, all their boost skills are at 10, and split over THREE DIFFERENT TREES.
It would be pretty easy to make a build with these that gave you cruisers going faster than destroyers, and I don't think that sounds right.
Here's a list of them all now I have the game open:
Combat:Helmsmanship(5) - Maximum Power giving +0/0/0/1/0.
Combat:Helmsmanship(10) - Dynamic Stabilization giving +0/0/1/0/1.
Leadership:Fleet Logistics(5) - Efficient Fueling giving +1/1/1/0/0 (the only rank 5 destroyer boost.)
Leadership:Fleet Logistics(10) - Optimized Navigation giving +1/1/0/1/0.
Leadership:Small Unit Tactics(10) - Small Unit Logistics giving +1/1/0/0/0.
Tech:Computer Systems(5) - Travel Route Algorithms giving +1/1/0/1/0.
Tech:Mechanical Engineering(10) - Burn Drive Mastery giving +0/0/1/0/1.
Tech:Applied Physics(5) - Burn Drive Miniaturization giving +1/1/0/0/0.
So, if we analyze these a bit, we find these results:
Destroyers can be boosted a maximum of +3 burn, but it requires 25 aptitude points and 30!! skillpoints.
Cruisers can be boosted by a maximum of +3 burn, but it only requires 20 aptitude points and 20 skillpoints
Capships get a +2 boost, and require 20 aptitude points and 20 skillpoints to get it.
Fighters/frigates are still linked, and get a total of +5, which you must pay only 15 aptitude but 30 skillpoints for. That said, you can get +4 for 10 and 20, see below.
Additionally, here's the breakdown of boosts available by skill tree:
Combat: +0/0/1/1/1
Leadership: +3/3/1/1/0
Tech: +2/2/1/1/1
This seems to indicate Tech being an all-round boost, leadership focussed on small ships primarily but a dip into Fleet logistics for +1 to everything, and Combat intended mostly just for big stuff.
May I suggest increasing these specializations while decreasing the total breadth of aptitudes and depth of skillpoints required to max a given class that a player is interested in?
I think the tree I like best in this setup is Leadership - keep that one mostly the same, though does Small Unit Logistics really deserve to be at 10? I think at 5 would be more fun without making it a big problem - frigate wolfpacks are already pretty much faster than anything else, and dropping the investment needed to get +2 frigates to 5 aptitude and 10 skillpoints is still way more than vanilla, without actually changing the type of fleet these ships can catch.
Destroyers are too hard to boost right now, and they're the natural step up from frigates - but this skill mod makes them very hard to use as you can't catch anything small enough to kill, and can't run from anything big enough to kill you.
First, swap some of the points around - give the destroyer boosts at Helmsmanship 5 and Applied Physics 5 - drop the destroyer boost at Mechanical Engineering 10.
Then, there are some choices - If you absolutely don't want a single point over vanilla, then I think you should move the destroyer bonus point out of Combat:Helmsmanship and into Tech somewhere - perhaps Mechanical Engineering 5, or maybe Computer Systems 5 (though this is then a very strong level and it's already giving more ordnance points and hull mods so everyone -already- loved this skill.)
Personally, I would say that your skill mod is already far enough away from vanilla that you don't strictly need to keep to the exact same set of bonuses. Destroyers could have +4 total without breaking the game, and if they continued to be spread over all three skill trees, it would be pretty unlikely that any but the most determined players would get it, and if they did, so what? They've got all three skills to max, let them have their +4 destroyers, eh? This would let you make destroyer boosts be easier to get everywhere - still push it down to Tech 5, but also have it at Combat 5 and Leadership 5 as well, with a further destroyer boost at Tech 10, perhaps exactly where it is now. I think Applied Physics 5 would be the best spot in my opinion, and this is the option I like the most.
It's still a bit weird that cruisers would get boosted before destroyers in the Tech skill, so if you really wanted to emphasise the speed differences you could swap the destroyer/cruiser boosts in Computer Systems and Mechanical Engineering, for +1/1/1/0/0 at 5 and +0/0/0/1/1 respectively.
This would mean destroyers would get a total of +4, but need 15 aptitude points and 20 skillpoints to get there - wheras fighters/frigates are still easier as they only need 10 aptitude and 20 skillpoints to get to +4.
Okay, end wall of text, what do you think? If I still feel this strongly about it tomorrow I'll try rewriting the scripts and try it out for a bit and report back - thanks for including the .java files in the .jar!