Regarding this being a problem, we have a difference of opinion.
I like the transition between from skirmish for objectives into the heavy hitters being deployed with those extra points - I think it works well, and very much as-designed.
There are also practical performance considerations, a 2d battlefield becoming too crowded, and extra ships not adding enough past a certain point, once the player doesn't get to interact with them very much. Certainly not enough to justify the tradeoffs involved in making that many more Onslaughts be able to duke it out entirely off-screen.
In general, you can probably expect to see somewhat smaller battles on the top end. The Hegemony SDF in the current version is probably bigger than what it ought to be, just as a temporary challenge until there are other means to provide it. If both sides in battle still have reserves after the initial objectives have been captured (and the second wave deployed), it's probably "too big".
Of course, you're free to have your own preferences, and mods may have very different ideas - which is why the battleSize setting is there.
Now, I'm not saying the current system is perfect. In particular, I'd like to take another look at how attack/defend/escape works.