Hmm... first things first... I have a question, SealedDarkness. Did you read Agastya's nitpicks?
Also, if you're looking for 10D sprites, you can extract them from Touhoumon Emerald, IIRC. Besides, I think you should remove the unnecessary Last Words (in other words, Last Word evolutions from characters that doeen't appear in Imperishable Night) and put the remaining Last Words (for example, where's LWriggle, LKeine (for both her human and Hakutaku form), LTewi and LKaguya?) In that matter, you can always rename the legendaries to something like... YUtsuho, HSuwako / TSuwako and NKanako (Y stands for Yatagarasu, H and T stands for Hisoutensoku, and N stands for Nuclear. The three initials stands for a common theme between them).
And if you're hesitant in removing Zero puppets... I think you can do this: Make Last Words accesible to the player, but as alternate forms (and with less BSTs,,, preferibly like between 550-580 BSTs, I dunno... maybe less), and make the Zero puppets in the BST range of 660-720 BSTs, or something plausible like that, but making them CPU-exclusive. The player shouldn't have access to playable Zero puppets... that would break the balance of the game. Besides... Zero Puppet and Last Word puppets should be only seen during the Post-game content for both games (in other words, post-league), so don't put them early in the game.
Besides, now we're talking about BSTs and balance, reduce the BSTs of Tensoku to 600 or less than 600, and give EFlandre another ability rather than Pure Power (Insanity or Intimidate, whatever ability works better with her). Also... look well into wonky movepools. There are some puppets with poor movepools considering their typing, and also, reconsider some changes on puppet types, like Sasha (Ghost / Dragon takes a better benefit of her physical attack) and Mitori (I have seen other hacks where she is Water / Steel. She doesn't have any reason for being Water / Dragon, besides the reason of Touhoumon hacks lacking Dragons).
The last thing I'll mention for now is a nitpick I have, and is the matter of music. A lot of the music from both Touhoumon games sounds... not so Pok?mon-ish... and some melodies sounds rather noisy and unfitting. Sure, I have to admit Aichiya did a good job in inserting .wav tracks, which I think, it's a strong point, but... I need to say this. I'm not fond of the usage of certain midi-ish tracks in both games for certain areas. For example, I don't like the Captain Murasa mix used as the Gym Leader music in Touhoumon World Link (the remix of Fate of Sixty Years in the style of RSE Gym Leader music fits it better), neither that crappy mix of Last Remote used in places like Mt.Chimney, which I prefer the theme used in the original RSE games instead. Anyway, try to look which melody would fit better in each area, if the original song used for that area in RSE, or a Pok?mon-ish Touhou arranged song, and besides... some areas in Kanto have the wrong music in some routes and areas. IIRC, Alice in Wonderland wasn't used until the postgame areas, and I think the gym leaders in Kanto should have the U.N.Owen was her? mix of the Kanto Gym Leader music used in the original 1.5 games, instead of the Captain Murasa theme I mentioned previously. Welp... the music matter could be a pain in the tail, but I'm just mentioning the issues I have with this aspect. If you think you can't do that, then no problem.
And... about Wobbuffet...
Howabout that Wobuffet, is it still on the banned tier? It only as a mere 405 total stats. Or does it's pathetic stats make it useless in 5th gen?
Not exactly... Wobbuffet in Gen V isn't actually in ubers... because of the changed mechanics for Encore (now it only last three turns always, not from three to five turns). That was a hard blow for him, besides... Gen V actually brought a hyper-offensive metagame, which makes harder to Wobbuffet to stand up easily against beasts like Chandelure and such (those are the reasons why Wobby is actually BL, in other words, banned from UU, and actually kind of usable in OU, but threatened easily by lots of threats). And speaking of Chandelure... his hidden ability is Shadow Tag, so when that ability will get released, he will prove to be an excellent Revenge Killer, trapping and killing almost any threat with his high Sp.Atk power and the right coverage moves, and IIRC, he's actually banned from the Dream World OU tier in Smogon, so... there you have it.
Well... that's all I need to say... at least for now.