OK, finally in here to look at stuff, got too preoccupied to answer things.
For Tom, the answer is likely closer to the games, probably with a touch of hybrid in there. I basically took the route the various adaptations did and made a silghtly AU-ish thing that's still (hopefully) true enough to canon while taking it's own spin on things.
YOLF was definitely right with the reference he picked up there, though.
Tom's predecessor was a direct reference to the the Mewtwo created on Cinnabar Island that's been frequenting caves since Red/Green/Blue. I decided to stay true to the games on that front at least. But yup, hopefully that explains it enough for now.
...Speaking of which, I probably need to update Tom's sheet now that the secret's out. ^_^"
And yeah, Archer's going to be more than a bit annoyed if he has to fix the kitchen again, so they'd better cool their jets in there. ...Especially since Hakuno's sleeping against his shoulder at this point. I'm assuming Ruu is just chilling in there watching TV still (Daiki come back to us ;_;).
And as for Kiyoshi's reactions to all the AU people... Admittedly I find it a bit odd too. Ryoko was pretty friendly to him, sure, but Cool Big Sis is one of her schticks. Plus he may actually exist in her world, I'm not actually for sure yet. Plus her circumstances are a bit different, but I'm still working out how that'll work, so that's not important for now.
...Regardless though, poor Lancer, he's going to have to help sort out yet
another mess. Plus he's not going to want the kitchen destroyed either, since not is it only his Landlady's kitchen, but the tea he's brewing for Mille to make her feel better is also in there. So with that, combined with everything else he's had to smooth over at this point, I suspect he's getting more than a bit grouchy with it at this point.