Similar to what TrootOrDair said, you may want to to stay where their roll towards will put them right in front of you and then attack the roll on reaction. Firebreath is a great option, for this and it's a good spacing tool so you can also throw it out as a poke. However, when you're looking for a kill, you can switch to down tilt. If you use it on reaction to a roll it will catch them rather easily and it'll usually get them offstage if it doesn't kill them outright. Actually even at low percents, down tilt isn't a bad punish, it won't kill but if they roll into both hits then they take a hefty 25% with a decent chance to trip. Dtilt is also good against players that like to run up and shield grab you on reaction when you mis-space your jab or Ftilt to zone them out, since if they reactively grab as soon as the first hit touches their shield, the second hit should beat the grab.
If your opponent is roll happy, then short hopped klaw is quite amazing, I've often found that if I follow the roll with the short hop klaw, even if I miss, it's fine because I can just klaw when I land and get the grab on them anyway, and if they rolled towards you instead it's whatever because they probably can't punish you anyway. You can use the klaw to move the opponent as close to the edge of the stage as possible. Getting the opponent cornered at the edge of the stage is generally what you'll want to be doing with Bowser, because most characters aren't able to safely back away from you anymore, which makes turtling more difficult, so you can space your attacks more freely and focus on punishing their escape attempts.