Thinking about it some more, one of the big issues with STO's space combat is that escorts, cruisers and science ships need to balanced against one another in the first place. After all, an escort shouldn't be fighting a cruiser one on one to begin with, much less winning.
So I was thinking of something like this:
Take Ship Size into Account:
We need proper classifiers for small, medium, large, and capital ships. Small ships do a lot less damage, and have a weak hull, but are harder to hit, medium do more damage and are a little easier to hit and so-on.
Your ability to hit a ship is based on size; so larger ships firing on smaller ones are more likely to miss than when firing on other ships of the same (or larger) size.
The result of this is that while an escort will struggle to bring down a capital ship alone, they will be fast, agile, and hard to hit.
Attack Patterns and "Wings"
Attack patterns should be worthless when applied to a single ship; after all what do they really achieve for one ship?
Instead we should be able to take a "wing" of ships based on our lead ship's size. The wing size is always four, but a small ship counts as one, a medium as two, a large as three, and a capital ship is too large to fight in a "wing". So for example if you're flying a medium ship you could pair up with another medium ship, or two small ones. You can't take wingmates larger than your own ship.
This would allow a group of escorts to balance out against a single capital ship, as their total damage would be close (but still lower, thanks to their innate defence bonus) than the capital ship's.
A wing of ships essentially functions like a single ship, except that your wingmates always suffer most of any damage received, becoming disabled when they suffer too much, but returning to the wing once they've sufficiently repaired themselves. The player ship meanwhile will be the last ship destroyed. It's worth noting that most effects for wingmates only apply if they are in formation (within 1km of your ship), so it's important to use ships that can keep up with you as abilities you use may not affect wingmates that fall behind, and wingmates that are "out of formation" will no longer function as a buffer for damage directed against you.
This feature also has the added side-effect of justifying why an escort may have a vice admiral aboard, as they would actually be commanding several ships. Meanwhile a vice admiral on capital ship is functioning as a flag-ship. The ability to take wingmates would grow with rank as players are able to take larger ships, and would replace the current fleet support ability.
A wing doesn't necessarily have to be comprised of identical ships, however player classes and ship type will have an impact on corresponding abilities. So only Science captains flying a wing of all science ships will be able to get the most out of science abilities, while the rest a penalty.
For example, if you had a wing of three small escorts with a small science ship then you would have a 75% bonus to tactical abilities and a 25% bonus to science abilities, with a further bonus depending upon your player class. While someone with four escorts may get more out of tactical abilities for such a formation, you would have added flexibility if you want to use science abilities.
On the issue of abilities, these would essentially all originate from your ship as the wing's flagship with self abilities affecting all ships in the wing that are in formation. However you would be able to assign bridge officers to each of your wingmate ships (one each). The slot that each wingmate ship has is based on its ship type and size, so a small science ship would have an Ensign science station, while a medium cruiser would have a Lieutenant engineering station. A capital ship (no wingmates) would essentially gain a bonus Lt. Commander station.
The AI for the wing would be simple; they will also strive to remain in formation (if possible), and when you fire weapons you essentially fire for the entire wing at once; they won't fire torpedoes until you do, and won't fire energy weapons until you do. All abilities are controlled by you; the only thing that wingmates really do for themselves is regenerate shields and hull.
However, if a wingmate falls out of formation, it will fire on any targets that present themselves while they try to rejoin the formation.
There would be some differences depending upon currently attack pattern. For example, with attack pattern beta your faster wingmates may break formation when under fire and fire at targets of opportunity such as projectiles and small craft. Pattern Beta will have your wingmates focus exclusively on one target, firing continuously (not waiting for you) while attack pattern alpha will have them wait and fire in conjunction with you for maximum effect.
While it would be a huge overhaul, I think a system like this would go a long way towards allowing balance to function meaningfully, with tiny escorts actually feeling like tiny escorts and capital ships only threatened when escorts come at them in groups, or when slugging it out against another capital ship.