I guess I'd like a "normalized" version of this with 100 vs 100 instead of CAP1 vs CAP2 ships. After all, I have no idea what the caps are for each, and the caps change with each Mk.
This would take double long to create, and I'm not sure where I would show this data. I've studied these numbers endlessly, and I'm pretty sure the current ones are the best representation of relative strength possible. It's multi-dimensional data that can't easily be represented as a series of single numbers, but these do the best of showing it.
Or, otherwise - show the caps in the Strong/Weak vs. so we can do the normalization in our heads.
There are too many units for you to really try to normalize to that level of detail, anyway, and that would just make the interface all that much more confusing. The unit caps are now shown on the hover tips -- second row -- but you'd have to look at the hover tip for the target versus the source.
My advice is to not worry about it to that level. If you have vampires, you can see that their cap is very low, so you can judge that you need fewer of them to get the same effect. If you have infiltrators, you know you need way more than usual to be effective. But that's about it.
For the numbers, 100% means that even if you are outnumbered, you will probably win -- your ships really ream the others. -99% means it probably doesn't matter how many ships you have, you will do really poorly against that enemy with your ship. It's meant to be a rough guide of best ships, not a formula for success (there's no such thing). It does a very good job of telling you the best ships for a given situation, and how relatively strong each of those best types are versus the type in question, and that's all it's supposed to do. If you want more, then that's the charts that Rev posted on the community wiki, which are hugely more time consuming to peruse (and, I think, less relevant during actual gameplay).
I mean, I used to think "Strong vs +50%" meant I could send 50 Fighters to kill 100 Cruisers. Now, all I know is that it means if I send ALL my fighters of a certain Mk against SOME RANDOM UNKNOWN NUMBER of Cruisers (of the same Mk) then I will have 50% of my fighters left after killing all the enemy Cruisers.
It means that if you send a reasonable number of fighters against a reasonable number of cruisers, they will have a good survival rate but won't escape nearly unscathed. Don't try to make this too concrete, especially because good (or poor) tactics, and/or other nearby ship class interactions, can completely blow this away. Unlike a TBS game, there isn't quite the precision of numbers in practice because of all the interactions and the subtleties of how tactics are played out. That's why this is just a rough guide, and can never be more than that. Even though the numbers are "right."
And, the AI isn't limited to a ship cap anyway. 
No, but they build in those proportions. That's important. A raid of infiltrators is always going to be about 6x larger than normal, whereas a wave of vampires is about 3x smaller than normal.
I am wondering if I am the only one who doesn't (or didn't) get this. I realize I'm not the master tactician that others are, but boy, have I been completely misunderstanding this game that I've been playing for months and for someone who doesn't usually consider himself a moron... I'm feeling pretty damn moronic.
I wouldn't worry about it -- the important thing is the relative powers here. You know which ships you prefer to use in a given situation, and which are not a good idea, and that's the important thing. The subtleties might help in specific close-call situations, but otherwise it's just important to know the order of preferences...
