Eh, maybe. That sort of decision isn't up to me anymore, though. Personally, no, I wouldn't consider it the same. Why? Because all he's recieving is an increase in size and strength, not some wholly new instant-kill special attack that comes at no real cost. In order to become Giga Bowser, he has to get his ass kicked pretty badly.

I'd consider Bowser turning into Giga Bowser more acceptable than Ganondorf transforming into Ganon. In his demonic warthog form, Ganon recieves a whole assload of new attacks and abilities, in addition to a size and strength increase.

Or what about Dante transfroming into Devil Trigger mode? That was allowed in the last tournament, and Dante recieves all kinds of badass extra attacks in that form.

So, no, if it was still my call, I'd let Bowser have his Giga form.