At the end of PM its Mario, Goombario, Kooper, Bombette, Parakarry, Bow, Watt, Sushi, and Lakilester along with the star spirits and Peach's wishes vs Bowser and the star rod plus the machine. We never see it happen of course but its implied they all worked together to beat him.
Sticker star Mario had Kersti, which I blame the ''not really needing'' on bad implementation of game mechanics
M&L when fought as Rookie he forgot all his techniques, in PiT its 4 on 2, in BiS Peach and starlow weakened Bowser, he even says that wasn't his A-game both times he is fought because of it.
Dream Team.....well its ending is frankly kinda rushed and even when they fight a super powerful enemy, they don't do the ''it can't be harmed until the plot says so'' thing.
As for the opening of Superstar saga.......oh boy, uh. Maybe because Luigi when flying into his back and it was a surprise so he wasn't properly prepared????