I just played through the game and got every ending, including the main ending.
I noticed a few issues:
1) When the 9th Man dies, his bracelet is still on the floor. Thus, the bombs do not destroy the bracelets. However, when Ace kills Fake-Snake, this is not held to be consistent. Fake-Snake has a 2 bracelet on, otherwise Ace wouldn't have been able to trigger the 3 door, but when he is exploded, no bracelet is found. Ace doesn't take it, since we never see Ace fess to it later. In the true ending, before Santa takes June hostage, everyone's like "welp, guess it's impossible for us all to get out alive". Clover stole the 0 bracelet from the captain, and everyone knows the rules word for word, so it's clear that everyone knows that bracelets off dead people will work*, so why didn't anyone pipe up with "Well, we just need a 2 bracelet, one of us should double back to Snake's corpse and get it"?
* 2) Translation issue? There are two ways to take off the bracelet. Get off the ship or die. When either happens, according to the in-game text, the bracelet will de-activate. This is not true. The bracelet does not deactivate, it just detaches. Its function still works fine.
3) The doors. In the Chapel, the rule is that once a door is activated, it can never again be activated. That's why the groups can't go through the 9 door twice in a row, and why it's significant that there are two separate 9 doors. However, in the incinerator in the past, the 9 door activates twice; once when Snake lets half the kids go, and once when Akane/June later on de-activates it after telepathically solving the sudoku puzzle. Moreover, when everyone wants to see Snake's body from the big hospital room, there's a big deal made out of how the un-numbered door has been wedged open, so that they "don't need to bother going through the 3 door." I'm virtually certain the game's text does not make reference to the "only go through once" rule. The doors can clearly be opened more than once, since the initial 5 door is opened when 9 gets killed and again later, and they also practice open one of the 9 doors in the chapel, and I think at least one other case. So does the door only lock to being permanently engaged when a group successfully gets through and authorizes on the DEAD?
4) Finally, I agree with other posters in this thread -- the Alice/Allice plot is sort of stupid. It's a bit of a red herring. She clearly exists, but her reveal at the end of the game has no significance whatsoever. I don't mind the supernatural gobblygook, but why is she wandering the Nevada desert? There was no Alice in Building Q, there was no Alice in the ship 9 years ago, so the real Alice thawed out at some past time... and... wandered the desert for no reason?
5) I actually get the time travel plot. Only Seven's "amnesia" makes no sense. Akane needs to survive to become Zero and set up the second game. Thus, Akane's survival is not "across multiple timelines". It's in the same timeline. So it's a paradox where she sees the future, survives, and then creates the future in order to ensure her past survival. No problem. Also explains why she's sick, like the 999 answers site says, it's when you diverge from the timeline and the paradox begins to collapse. But why don't Seven and Snake make a big deal out of it? According to the 999 answers site, Seven has an implanted fake memory--what the christ, this is a terrible explanation and clearly not satisfactory. But how could Seven be in on it? He stays with the main team during the True Ending, rather than running away with Santa and Akane. Is he not aware that he, too, is an accomplice to multiple murder? Sure he plays by his own rules, but what's his plan if he turns in Ace? To admit he was part of an elaborate kidnap scheme just to catch Ace to then turn him over to Justice? This is silly. But assume we disregard Seven, and Snake is still a problem. But Snake's approach doesn't make sense. He says a girl named Akane died. She did not. Blind or not, he would have been aware that she survived. Which means Snake needs to be in on it too? This makes absolutely no sense.
6) It makes no sense that no one catches up to Santa+Akane. This is not a satisfying resolution. Why is Akane going on the run? She is scared of being caught and punished for her actions? This makes no sense. Either the triple murder is part of the future she perceived (in which case, her actions were unavoidable and she has no reason to feel guilt, although she is trading three bad lives for her own, so the utilitarian question is interesting there) OR she didn't need to kill those people, but chose to anyway, in which case her conscience is apparently clear. Is she worried about answering to the law or to Junpei? She clearly has love for Junpei, at least as strong as the love we see between her and Santa... Why are Santa and Akane on the run at all? Shouldn't they have at least stuck around to see whether or not the whole thing went over okay with everyone else? Also, Santa and Akane are multi-millionaires who rig this whole thing up (see: 999 Answers, Santa mentioning his stock market money)--and according to the 999 answers, they had dozens of helpers, which is logical... so how could they run from the law? If they believed they needed to make a run for it because Seven (who, again, needs to basically be in on it for the plot to work?) is going to NARC them out, won't some of their many employees narc them out? Or their asset trail? Won't they be wanted international fugitives, since their names will be publicized?
7) How did Santa and Akane get Building Q from the pharmaceutical company? Why didn't the pharmaceutical company bulldoze it after the last Nonagram game? They kept around essentially the world's largest collection of evidence that they committed massive illegal acts? If they did keep it, why would they sell it without stripping it down? Or did Santa and Akane build a replica of Building Q, not the real thing? Zuh?
8) Why was Ace offered the chance to repent? This would not have satisfied the future paradox. It seems like an awfully big gamble to tell Ace that the option is there, even if you know he's a horrible guy and he's not going to take it. The letter could have read "To survive the Nonagram game, you must meet with a man in the Captain's Quarters. Tell no one.", and this plan would have been better.
9) The whole "childhood lovers drifted apart because they went to separate schools" is absurd. The game is set in the present tense. The childhood scenes are set in something like 2007. You're telling me two ten year olds couldn't keep in touch? Why not? This makes no sense. That plot is incredibly thin when you're talking 1950 and people moving to different countries, it's farce in 2007 when you're talking different schools maybe even in the same city.
