I'll take a look with Zyrthofar's editor later, as far as I could tell from playing nothing was changed other than the PinkPuffs. The funny thing is that I never encountered that change before you brought it to my attention, but I ended up running into them in two of the three rooms while testing FF2 *is* ET without even trying to.
"Enc. Loc. Set $4C" has slot 5 changed from 1 King-Ryu, 1 Ging-Ryu to 1 Tricker and slot 7 changed from 1 Tricker to 3 PinkPuff, 2 PinkPuff. None of the other encounter sets had any changes that I could see. I'll check the actual locations later, don't really have the time at the moment.
One thing I remembered though, the Avenger is guarded by 4 Malboros in FF4 and 2 in FF2us and ET.
We have EVEN MORE themes now, but some old ones are gone...