ACE:
Ace is pretty high in the suspect list for a few reasons.
1. He didn't care that we switched our papers in the Axe ending. But this could just be reflective of his personality.
2. By the end of the Axe ending he takes Lotus away knowing that a Zero watch exists. This, along with the Knife ending gives me reason to suspect that he is the murderer. However, there's two holes to this line of reasoning.
Can a watch work on a door without the user?
If he is the murderer, it doesn't mean he's Zero.
3. His show of "altruism" says a few things: Was it necessary he do so? Why were there no signs of the side effects when he woke up? The first point could be addressed with a simple "he did it to give them no choice." And I'm pretty convinced that's the case, and if that were the case then, given that I take the second point within face value... was it actually anaesthetic?
4. He knows a lot about boats. But that's not much to go on really.
SNAKE:
Probably the person I'm most suspicious of. There's a lot to him that you can't be sure about. Him and Clover hide things and they share no resemblance at all, perhaps it's anime eccentrics working again but I like to think the difference in design is on purpose. Yet they're most probably just not related and that's it, they still hide things though. Clover made this pretty obvious in the Knife Ending when she reached to tell Junpei something and then shied away (there's other cases too.)
However not a lot of what he does is suspicious and in fact... he dies and it seems that's always a flag. But if Agatha Christie taught me anything is that just because a character is presumed dead doesn't in fact mean he's actually dead.
The most blowhard crackpot I had at the moment is his Braille note which gives him (presuming he's Zero) the initiative over everyone. Who else could read Braille? Nobody.
If he wanted to he could feed us false information he could easily do so. It could be absolutely gibberish and nobody would know.
Too bad I can't remember a lot of his conversations in the Axe Ending. They could strengthen all this conjecture.
Also game wise it's pretty suspicious that he's a flagged death (as far as I know.) Obviously Clover's yandere massacre and its victims were not his murderers. Unless I'm given reason to suspect that they had reason it'd be pretty counter productive to waste anyone from the Nonary Game.
JUNE:
Now June obviously has a big part to play here seeing as she's the love interest but also given her interest in symbology (if that's the correct terminology?) And her connection to the Coffin and Hieroglyphics found in both the Knife and Axe ending.
I want to go ahead and say June is 'bland' on purpose and there's a big side to her we don't know. She's the typical blushing maiden that teases us with sexual provocation from time to time and looks cute as f*ck.
Geth and people I trust are like "PLAY.THIS.GAME." I'm sure June is using Junpei somehow.
Anyway it's all conjecture, everything I've said so far has been conjecture and the following is big crackpot I have in my head.
ALLICE, the name and the numbers each letter represents all give us the digital root of 6
The Puzzle in the Cargo room wanted 15, 1+5 = 6.
It's crackpot as f*ck but I'm using my brain for sh*tty stuff like that since it's fun to be suspicious of everyone again.
Besides, I can never truly be sure of anyone until I'm absolutely certain of Zero's motives.