I just can't see it being Rover or Isabelle.
Rover:
1) Rover is never mentioned by any animal ever. Nobody knows him. He has never been seen outside of the bus/train you rode in on. There is no allusion to him whatsoever. You could argue that Rover is a "world traveler" and such, but if he were such a traveler, don't you think your animals would mention it?
2) Rover obviously doesn't FOR SURE know what your town looks like. Yes he "happens to have a map" but it's one of four. So why, pray tell, would you ask someone to be a mayor when they HAVEN'T EVEN BEEN THERE BEFORE? If Rover were truly to be your town's mayor, surely he'd know right away what the town should look like! This basically shows that Rover a) has no knowledge of your town and b) would probably not know of Tortimer or anything, since if Tortimer knew Rover and offered him a job as mayor, surely the two would have met in said town.
3) That question is hardly proof. He could have simply been getting ahead of himself, but forgot his manners halfway through and quickly stopped himself in order to be polite and get your name first.
4) Would you really be stupid enough to simply pass your responsibilities on to some random kid? I mean I know people hate Rover but the guy isn't mental.
Now, as for Isabelle:
1) Do you really think she's capable of lying? The biggest lie she ever told was "I'M NOT SLEEPING!" when you can build the Dream Suite, but even then she quickly fesses up and admits to it. That's not even a legit lie so much as it's just some disorientation due to nodding off. So yeah. Isabelle is honest to a fault. She wouldn't lie and withhold information in order to fool the ENTIRE VILLAGE and yourself.
2) Isabelle is DAMNED RESPONSIBLE. Of all people to shirk responsibility, Isabelle would not. If you leave your game unattended for long enough, Isabelle will actually say something along the lines of "I've tried to run everything while you were gone." But she will also tell you that you are needed, and that things aren't the same when you're not running the joint. This not only points to her being entirely capable of stepping up and taking responsibility, but also recognizing her own title and not wearing shoes she can't fit into. She's just NOT the mayor.
3) If I haven't convinced you already, as stated when you begin the game, it is known that the mayor would be arriving on the train that day. This basically means nobody currently in the village could have been due to be mayor. Yes I said Tom Nook was "more believable" but he's pretty much obsolete too.
I still think Tom Nook is Zipper though lmao.
Honestly I'd be more inclined to believe PHINEAS is supposedly the mayor over most of these theories. He's respected, gentlemanly, well known, and he watches all of your progress and gives you badges for your wonderful work. Much more plausible of a mayor IMO (now that I spell it out that actually is sorta plausible haha, but Phineas is probably too old to consider taking office).
To me it'd be more believable if
A) Tortimer had a son or relative ready to take office, but they either did not make it or did not really want that job. Thus when you arrive, it's a happy coincidence how things turned out, and you earn the old Mayor's approval and the new Mayor's best wishes. This would explain why Tortimer isn't at all shocked when he sees you as the Mayor during your first meeting.
B) Another Villager, just like you, is supposed to take over. But said villager ended up in another town. This results in a mixup in which the other villager accepts this turn of events, and sends you his/her letter of well wishes.
I don't really think either of those are super believable either, but I'm sorry, I just can't believe Isabelle or Rover were due to be Mayor. Rover makes no sense, and you'd have to perform a complete 180 on Isabelle's personality to fit her into a theory regarding her. So yeah, not buying it.
- - - Post Merge - - -
Also before people jump on it yes I know Tom Nook can't be zipper since he is still in his shop that day. It's probably just some poor guy in a costume being paid minimum wage to act happy. It's just hilarious to think of him in that suit.
Also note I'm not trying to be a killjoy. I love theories. Just I think they're a lot more entertaining if they're like...plausible.