I think the most painful cut for me was the Pokémon Trainer from Brawl.
I still remember when I checked Smash's website the day they were announced. That was one of the few times I actually was excited and surprised about an addition, and I fell in love with them in gameplay. They also had one of the most unique gimmicks (stamina), which made them really fun to play as. Also that Red was in the background of every stage directing his 'mons to fight - how cool was that?
Since then, I've always tried to get a team of those three in my main series Pokémon games, just because I liked their dynamic together.
Charizard was back, but Squirtle and Ivysaur were nowhere to be found, possibly because they cut the transformation mechanic. It's time for the rest of the team to join back up!