Electric Yo-Yo was easy to fix, it was crashing because of a synchronization issue between the two CPUs - increasing interleaving fixed the problem.
Looking at the schematics surely was interesting, for example I discovered that the video ROM bank latch (which is a late addition only present in Zookeeper) is mapped on a mirror address of the diagnostic LED / palette bank latch. This explains why they oddly mapped the ROM banking bit on data bit 2, instead of the more obvious bit 0. That's because bits 0 and 1 are the ones that control the palette bank, and since the ROM bank latch is at a mirror address of the palette bank latch, whenver the former is written to, the latter is affected as well. So whenever the game wants to set the ROM bank, it also copies the palette bank in bits 0 and 1 to avoid unwanted side effects.