Ooo, here's an idea. You could even expand it so that ships at lower levels gain more XP than ones at higher levels. Sure, you could still send in a Lv1 Kol with a couple Lv5s, but the Kol would get a lot more XP in the long run, but not 100%. Think of it as RPG style play - weaker ships get more XP for destroying higher-level ones (if this is already in the game, it should be emphasized a bit more). This would essentially solve the problem as the low level ships would get a good (but reduced, as to be fair) chunk of the xp with the higher level ships getting a low amount further reduced by the 50/50 (or 33/33/33) split.
This is indirectly in the game already. Higher level capitals are worth more, and since lower level ships need much less xp to level up, destroying a high level capital to them is worth more than if a high level capital destroyed it. Essentially, if a level 1 capital needs 300xp to level, and say a level 8 needs 2000 (just example numbers), then destroying a capital worth 300 would mean a lot more to the level 1 than the level 8. Even if the xp is split evenly (the level 1 gets 150 and the level 8 gets 150), that still maintains the more immediate benefit to the lower level ship.
Given that there's a very limited number of capital ships in any given game compared to the other ship types and not a continuous stream as is the case in the RPGs you refer it, I think this indirect system works well enough. And it only works because progressively more xp is needed for the next level. If it was always a flat amount, then it wouldn't work
That said, I also don't see a reason why max level capital ships should siphon xp away from the rest, I think they shouldn't be included in the split at all. But, that may already be happening
