The problem is that they nerfed Giga Bowser hard for "balance".
Compare how he is as a boss in Melee to how he's a Final Smash, and you'll see what I mean.
Still, nerfing Giga Bowser's power is unacceptable when you look at what the Super Mushroom is capable of doing now. That item boosts direct attack damage to 1.56x in standard matches, which makes Bowser hit harder than Giga Bowser with almost any attack, despite still being shorter in size; heck, even when Bowser is normal-sized, Giga Bowser's b-air deals
less damage than Bowser's b-air.
Additionally, in a giant special smash, while fighters will normally use a 1.64x damage multiplier for their direct attacks, the Super Mushroom increases that damage multiplier to 3.08x, which is a drastically stronger attack boost than in Super Smash Bros. Brawl. And since Giga Bowser can't use size changing items, that kind of damage multiplier is beyond his reach.
It should also be noted that when you look at Giga Mac, in a giant special smash, he can still hit harder than a Little Mac who's using a 3.08x damage multiplier. And the reasoning for that is because most of Giga Mac's attacks deal 2x more damage than Little Mac's attacks; in other words, 2 * 1.64 = 3.28. And much like with Giga Bowser, Giga Mac is unaffected by size changing items.
At least in the case of Wario-Man and Mega Lucario, because they're able to use size changing items, their power boosts don't have to be too drastic.
Wario-Man's greatest strength is not so much brute strength, but being able to utilize a ridiculous air game, and having practically no ending lag for most of his attacks. As such, Wario-Man doesn't necessarily have to hit harder than a Wario who picks up a Super Mushroom, since he can use Super Mushrooms as well.
As for Mega Lucario, while Lucario can potentially deal just as much damage as Mega Lucario when the right circumstances are in play, Mega Lucario doesn't have to worry about flinching from opposing attacks, enabling it to take better advantage of the maximum aura damage multiplier. And when combined with a Super Mushroom, Mega Lucario basically becomes one of the most devastating fighters in the Super Smash Bros. series when it comes to dealing damage, especially in a giant special smash.
Anyway, a Final Smash is supposed to be on the powerful side, and I just don't understand the logic of Bowser getting better results with a Super Mushroom than by changing into Giga Bowser (who can't use Super Mushrooms at all). Also, if memory serves me right, competitive play turns off items, so Final Smashes will never occur in such matches anyway.