OK, now for my "long awaited" completion of my post.
WARNING: Lots of mathematic reasoning ahead,
There are two factors (that I can think of) that make differing caps with same cap HP not the same in terms of matchups. (Armor is being ignored, as that more influences offensive effectiveness more than survivability over changes in ship cap, all other things being equal, especially if the armor mechanics are being changed)
1. The overkill vs. focus fire effect. This makes larger caps, lesser individual HP forces stronger, as more damage is more likely to be wasted by heavy hitters.
2. The diminishing DPS effect. This makes smaller caps, larger individual HP forces stronger, as it takes more to take out one ship and thus it takes more to reduce a fleet's DPS by any amount. (AOE also falls under this category)
So basically, there are thing influencing the cap/individual health tradeoff and how it relates to overall effectiveness both ways.
However, at least in the current balance, factor 2 has an overall average greater effect than factor 1. However, because of factor one, low cap ship's shouldn't be penalized too much.
Also complicating things, the magnitudes of how much 1 and 2 matter are non linear. For below average caps, factor 1 is about linear, but for above average caps, it starts out about linear, but will "accelerate" upwards as cap gets bigger. (Imagine 98 vs 1 billion ships, even if of those 1 billion ships were scaled down accordingly)
However, I wouldn't worry about that. If my thought experiments are right, it would take like 5x average cap before you really start seeing the super-linear nature of factor 1 begin to be noticeable. Nothing in the game currently has more than 3x the average cap, meaning adjusting for this factor linearly would be a decent approximation.
A similar story for factor 2, but with directionality reversed (noticeably super-linear for less than cap, about linear for more than average cap). However, the point where the super-linear case would start noticeably showing around 5-10 (numbers, not multipliers), which DOES happen in the game.
Taking all this together, at average cap (98 on medium caps), the cap health "adjustment" would be 1x (to form a baseline), as the cap goes up and individual health goes down, the cap health "adjustment" would go up (due to factor 2's greater influence) about linearly (but slowly), but then at around 4x cap, would start to taper off some (due to factor 1's super linear nature starting to assert itself), and then once you really get high, would actually start decreasing back to 1x (due to factor 1's super linear nature finally overtaking factor 2). As mentioned, you don't really have to bother modeling this, as there are no 4x of average caps in the game currently.
A similar effect as cap goes down and individual health goes up. The cap health adjustment would go dow about linearly (probably at a slower pace than it went up when caps went up), until around 15 or so where it would taper off and decrease more slowly, until around 5, where it would actually start heading back up to 1x, getting close to 1x once cap reaches 1.
I can try to graph this is you want.
Some critical points need to be established though. Let N be the average ship cap. Then, with the cap health adjustment needed to offset utility change over ship cap, (function H), with H(N) = 1, what would H(N/2), H(2N/3) (or possibly H(3N/4)), H(10), H(5), H(1), and H(2N) be? (As mentioned, for now, we can model H(x) for x>N pretty much linearly, as caps don't really get big enough to start hitting that "tapering off" point where the wasted overkill effect starts to overcome the reduction in DPS per ship loss effect, unless someone can show that 3.2x, it does start to come into play significantly, in which case we will need some more "shape defining" points to be determined for H(x) for x > N).
Also, I am still of the opinion that the 50/50 rule (which, expressed in terms above, H(2N) = 2, H(1)=.5) is a bit much. Something closer to 25/80 seems more like it (H(2N) = 1.25, H(1) = .8
)
But then again, someone will need to figure out some more quantitive data about how much factor 1 and factor 2 come into play, especially with regards to each other, to figure out where the "critical points" of how utility varies over ship cap.
See, balancing is easy.