So Bowser's Adrenaline system is in "Rump Command". Researching Adrenal Glands shows in a normal person they're above the kidneys, which are still around midriff area, I still wondered: Why the Rump? Then I realized: Perhaps they're just showing that they're getting Bowser off his ass, you know, "Get off your ass", or "Get your ass in gear". But then I wondered: Why does it make him grow so big? Has that really ever been explained? Which gives another possible reason for its location: Mayhaps it's a subtle hint at its being an Ass Pull. Or perhaps I'm just a loon.
Could be a reference to the Heisei Godzilla VS Mechagodzilla, where Godzilla's regeneration and strength are sourced in a secondary hindbrain in his lower back.
What we find in Bowser's brain further confirms his status as the series' Anti-Villain: not only is Peach one of the most carefully preserved memories in it, but she is also the shape the archive's caretaker takes to communicate with non-threats. Also, his subconscious takes Mario and Luigi's shape when it comes to protecting it. Worthy Opponent much?
Fridge Horror example: It's made pretty clear in the game that all of Bowser's minions are attacking him because they're being hypnotized by Fawful. When you get to Bowser's castle, there are sick thwomps. It was hard for this troper not to feel sorry for them from the first battle: they can barely attack on their own and get frequent headaches which can bring their health down. Fridge Horror comes when you realize that they are ALSO being hypnotized! So these sick, aching thwomps are being killed-excuse me- KOd by Bowser and they're not even willingly trying to fight him. AND, we learned in Mario & Luigi: Partners in Time that not all thwomps are bad, and some would have helped the Mario Brothers.
There's also the Jailbots in the same area as above. Bowser's minons (Goombas and Bob-ombs) are trapped in what are basically mobile assault jails, watching helplessly as the robot they're jailed in assault Bowser. This is painfully obvious when Bowser free them from the Jailbots and the minions are happy to see Bowser and reward him. Imagine, they're the ones that are too loyal to be brainwashed by Fawful. AND you can use Bowser's flame breath on them... Which makes Goombas twitch in pain. And makes your loyal bob-ombs explode and basically sacrifice it to destroy his Jailbot.
Fighting them with the Mario Brothers will just result them in running away though (they won't even heal them).
On the other hand, the bomb-om didn't really have any prospects aside from blowing up anyway, as it's literately all they are good for in combat, which or less means you're using them for what they were designed for.
A bit of Fridge Horror for Bowser's Castle, as the Shroobs were frozen there. What was Bowser planning on doing with those Shroobs? Was he (or someone associated with him) planning on testing the Shroobs and make it sound like an isolated incident.
Fridge Brilliance: Why doesn't Bowser have his throwing hammers in this game? Because said hammers are probably manufactured in his castle, and his castle has been taken over by Fawful.
The Wiggler gets angry at Bowser for pulling the giga-carrot AND eating it, despite the fact that he told Bowser to eat it. But then you consider that he gave Bowser 1 minute to eat the whole thing, and (thanks to Mario and Luigi breaking up the pieces in his belly) he succeeded in less than that. The Wiggler was probably furious that he actually succeeded at what he thought was an impossible challenge, and in doing so destroyed his family's pride and joy.
Bowser's Intruder Fangs give him two attacks per turn. Now, there are quite a number of turn-based RPG games where bosses gain multiple attacks in one turn. Given that Bowser is usually a boss in most other Mario games, this actually fits.
And you get them when you reach Final Boss rank to boot. Final bosses almost always get to attack twice in a row in RPG's.