well you DEFINITELY dont want to be playing on FD, EVER. EVER EVER EVER. generally bowser is better on the really small stages (yoshi's comes to mind obviously) some people think japes is a good bowser stage because of some of my vids, its really just a mediocre bowser stage at best, the ceiling is RIDCULOUSLY high, although you do have invincibility for almost half the match lol
i dunno, i like taking people to battlefield also it can screw up their sweetspots but it doesn't erally harm bowser, i dont mind mute city actually, even though you dont have ledges to grab... i take people to brinstar a lot, i just really like that stage for some reason i think that one is more personal preference....
generally yoshi's should be a standard counter pick, if you cant do that i go battlefield or brinstar, and if for whatever reason those weren't allowed then from there it'd be dependant on who you are playing against, i know people like FoD and stuff like that, but just be sure to avoid FD at all costs.
other stages... corneria is generally to big but bowser has some nice tricks under the wing on the right including auto cancels on the fortress uhh... just look for preference beyond yoshis story is my best advice, everyone has a particular style and stage they like
i didn't expect a question so soon haha