I was far less thorough this time because it turns out I don't really like BG2 all that much. Good to know after 20 years. But here goes...
General observation: even though BG:EE and BG2:EE share engine and therefore option menus, in both the options are in different order making it hard to set them both up in the same way. (Shared settings would be ideal)
General observation: there is no option to turn off critical hit screen shake in EITHER game.
General observation: all the ring icons in BG2EE seem to be upsized. Look about 50% larger? Was that always a thing? They look like crap.
In Irenicus Dungeon 1, the EE weapon import didn't work at all. I ended BGEE with The Burning Earth; it appeared in the chest next to the Sewage Golem. Malaaq himself never spawned - clicking on his lamp makes the sound but no animation and he doesn't appear. Needless to say, his quest was unfinishable.
Sewage Golem remains invincible, even after opening the doors.
In any area that has a "welcome message" on arrival - for example the Lower Tombs, in Pai'Na's lair, Southern Tombs, and Planar Prison - the message repeats every time you load the game in the area.
Encounter with Neera cannot be avoided. All EE NPCs in BGEE could be avoided.
Chaotic Neutral character was assigned the Temple of Talos for Temple-related quests(Cult of the Eyeless and follow-ups) Could be WAD though.
After you get the Thieves' Guild as a stronghold, the name tag is added to its current name tag rather than overwritten, so you end up with "Mae'var's Thief Stronghold CHARNAME's Thief Stronghold"
Gaal does not capitalize pronouns when talking about the Unseeing Eye. I think he should, given that he sees it as a god.
The irenicus cutscene/dream which begins with "Stand." - you don't actually start lying down.
The Improved Haste/Invisibility of Ring of Gaxx are still broken - they cast at "level 0" and therefore last very short time. Also, the Disease immunity doesn't show up on character sheet.
Game hard crashes when dual-wielding and polymorphing into a Flind. Could also be the case in BGEE but like hell I'm crashing my PC to check that.
"Seek Out and Investigate the Fallen Paladins" quest still likely not working as intended. You get 7500XP for trying to join and Reynald NOT leaving, and everything points to how the opposite should be the case.
After you fight and kill Neb, you're automatically hit with a Restoration spell which fatigues you.
In Planar Prison, the Warden's pet Wyvern's wind clapping sound persists after its death(repeat from BGEE's Greater Wyverns)
Trademeet: Lurraxol family guards don't aggro together when you attack one of them.
Ruined Temple: Anath hailed me normally, but by the time I got into the Wolf Cave(which was AFTER I cleared the shadows from the entrance to the dungeon) she was already dead in her human form. Technically it should be the case, since she's scripted to die as you approach the entrance to the dungeon, but still...
Shadow Patrick has two Composite Bows.
Even after you kill the Shadow Lord and light up the Ruined Temple area, the decription of the "dragon hole" doesn't change and it still talks about unpenetrable darkness.
Umar Hills: Some of Madulf's buddies use weapons they don't even have animations for(i.e. Gnoll fires a bow by swinging his halberd, and the Orc has a crossbow which he fires like a bow) and if you attack Madulf's buddies he joins the fight on YOUR side.
Cleric Stronghold, Talos edition: Acolyte Vilon, the questgiver, uses a "kind cleric" voice set, which is entirely unfitting("I welcome you with outstretched hand..." said no Talos Clerc ever)
Cleric Stronghold, Talos edition: something about third and fourth steps doesn't seem to work as intended. According to the otherwise excellent DSimpson's walkthrough, you're supposed to kill Renia for her lack of faith, take her head, then kill Cotirso and frame him for murder of Renia. Hovewer Renia doesn't drop her head, and in fact such item doesn't exist in the game files. Cotirso's head exists, but he doesn't drop it either, and even after spawning it with a console I couldn't give it to the Inspector anyway.
Ranger Stronghold: "Tombelthen Soldiers" are literally called just that - plural, "Soldiers"
"Night falls" movie plays in Temple Ruins area.
Once you free the Dryads in Windspear Hills, one of them still has the Genie Bottle.
Vampiric Mist has footstep sounds.
All Orcs seem to carry bastard swords, even though their models clearly use axes. Flaylan(Domain of the Dragon) actually has a spear! Archer Orcs have melee attack animations with a dagger, but carry no daggers.
Hobgoblin Shamans carry maces, even though their models use swords like all hobs. It's a "Shaman" not a "Cleric" anyway.
When joining the Most Noble blah blah order as part of Paladin Stronghold, Sir William Reirrac says "Behind me is your private room" even as he is standing smack in the middle of the main hall.
Paladin Stronghold: When talking to "squatters" in Umar Hills, Crolus approaches you over and over but doesn't say anything.
The "Cowled Enforcer" who teleports first after you cast spells in Athkatla is only worth 120XP.
Twisted Rune: Revanek, the level 19 Fighter has absolutely no equipment and attacks you just with his fists. Personal idea: make him a Monk, as he's already Lawful Evil.
Large Orogs(the one with horned helmets) use halberds, even though their models hold swords as usual.
In the Mind Flayer dungeon hidden in the Athkatla Sewers, you can get stuck on the first door by opening it when standing next to northern wall and then enemies blocking it from being closed again.
Innkeeper in Brynnlaw has a voice set with lines complaining about mercenaries. Surely not in Brynnlaw...
Rakshasas wield longswords rather than scimitars.
Two copies of First Journal of Jon Irenicus exist, one in the "storage" in the map with the soul-sucking machine, the other in his private quarters in Spellhold foyer.
Saemon Havarian says the ship you arriven on Brynnlaw with was "scuttled" even though obviously it's still there - well to be fair it could be different, but identically looking ship.
During the first dream after losing your soul, when you're shown the power of the Slayer, you get both Untouchable and Godlike achievements.
Saemon can be killed during the Githyanki boarding.
In Underwater City, you can pickpocket second Silver Blade from Baron Thelokassyil.
Piergeiron, one of the Forgotten Realms setting legends, who appears as part of the Imps riddle in Underwater City, uses Noober's voice set. Heya!
Royal High Priestess Senityili and Captain Feerlattyis both automatically die when you get the fake heart from Prince Villynaty but... why exactly does this happen?
Similarly, once you turn against Prince Villynaty AFTER killing the king, his High Priestess is invincible and runs away. No reason for this to be the case.
Speaking of which, the Golem you put together as part of Planar Sphere quest, whose only job is to open few doors, is ALSO invincible, even after it kills the Elder Orb.
There's a weird lone Mind Flayer in an inaccessible part of Underdark, south from the entrance to Western Caves. I assume that he's the Phaere's guard, since originally all Mind Flayers in that fight were "summoned" and so died instantly to Death spell. Well, that's fine, just make sure you can't see him.
Solaufein exists in several versions, and by pickpocketing him on every occassion I gathered a total of 6 Piwawfi Cloaks.
When Phaere sends you to kill the Svirfneblin, you can ask the leader for the helmet and then kill him and get another helmet.
All Drow in House Jae'llat have normal elf skin colors.
All three tunnels with "powerful creatures" you have to kill for the summoning ritual are badly mismatched. To recap, you enter the Illithid Lair from the north, you enter the Kuo-Toa/exit area from the west, and you enter the Beholder lair from south-west, though north-west entrance also exists - it's just unused. Except the Kuo-Toa/exit area is "West Tunnels"(so when you enter, you do instant 180 degree turn) and Southern Tunnels are the Beholder lair, so again you do instant 180 degrees. Furthermore, it makes no sense for the Western Tunnels to be the Kuo-Toa ones, as all Kuo-Toa are in south-eastern part of the main Underdark map behind the bridge. Finally, transition to Southern Tunnels shows a stair icon rather than the usual wheel icon. For it all to make the most sense: the Kuo-Toa/exit area should be Eastern Tunnels, the Beholder lair should stay as Southern Tunnels and possibly use the northwestern entrance instead, and the Illithid area should be Western Tunnels.
The transition zone to Southern Tunnels from the main Underdark area is away from the map edge.
Also, in Western Tunnels, the level transition zone is away from the map edge.
In many cases, Drow fighters - who only have animations wielding swords - are equipped with Drow Flails instead.
On the uppermost level of Ust Natha, the area change zone is not even close to the actual doorway.
Drow Mages only carry basic wood quarterstaves, even though Drow Adamantite Chain +5 is apparently a common item in the Underdark.
Both the Troll and Spirit Troll slaves in Ust Natha Bazaar don't have the troll "dying" script, they just die when their HP reaches 0.
After escaping the Underdark, in the Elven temple ruins, War Elves aggro individually and neutral War Elves will attack the War Elves you aggro'd(and vice versa)
Speaking of which, the Elven forces in the temple are pathetic. They only carry the most basic unenchanted stuff even though the Drow have +3/+5 everything.
One of Drizzt's buddies drops a second Tansheron's Bow, with different icon.
You don't actually have to travel through any of the three wilderness areas(Small Teeth Pass, North Forest) to get to Athkatla from Underdark Exit. Was this always the case? Weird.
Killing Aran Linvail in Chapter 6 will add a journal entry about working for Bodhi.
Time of day will automatically change to night when you enter the Temple District in Chapter 6. Lame.
The scripted spider ambush as you approach the Spider Lair in Lower Tombs still happens, even in Chapter 6 when spiders don't spawn in the area anymore.
"Meck", the messenger from Playhouse stronghold, will glitch and spawn multiple times if you do the Playhouse stuff before he tells you about it.
During the last apprentice test as part of the Planar Sphere stronghold, Morul describes the Staff of the Magi as "armor for a mage", even though it's a staff.
When you enter Suldanesselar for the first time and Elhan hails you, you can immediately reply "I have to hurry to Demin" even though he didn't even tell you who Demin is yet.
In Suldanesselar the Maharajah(Rakshasa on steroids) still drop long swords.
Raamilat, the Drow mage who uses the drow fighter model, wields a quarterstaff even though again, drow fighters only have sword animations.
Cloak of Mirroring animation is not continuous.