You should only be seeing at most one cross-planet attack at a time... that might be paired with other normal waves (which are pretty large that late in the game, I imagine). Having 3,000 ships in a cross-planet attack is very unlucky, those range between 1,000 and 3,000 ships usually. You might try reloading that save again and see if you fare any better now that you are better prepared.
The AI did indeed receive a big upgrade in how it works, and one downside is that some of the balance of really-long-and-on-the-brink savegames from prior versions might suddenly become unwinnable if you were already in just a moderate position, rather than a position of strength.
With a game that long, the AI is bound to be as entrenched as all get out, and now it's going to be coming back with a vengeance.
Also of note: in prior updates, if you had been making it that far into the game it's quite possible that the AI was stalling out and thus not really playing much. In the last update that was fixed, so now the AI is fully "awake" and after you. So it's quite possible that there were a lot of freed ships all over the place in your map that seemed dormant but really should have been attacking you if the AI was not stalled out. If you're seeing massive numbers of ships inflowing constantly, then that's probably what had happened. That's a very unfortunate side effect of the bug in the past release, it would have made things (much) easier than they should have been, and the fixed update would then be pretty apocalyptic.
