I hate Samus' grab. Its active hitbox as more frames than any other character with a tether grab. Its FAF is also the highest of any tether grab. Even Zero Suit Samus' FAF, with the exception of dash grab, is better. In the order of tether grabs from best to worst, it goes from Lucas, Toon Link, Link, Zero Suit Samus, and Samus. Because apparently, futuristic tech is slower than some kid throwing a snake rope and Medieval-inspired tech. Right, makes a lot of sense.
I hate Samus' projectiles. Charge Shot can be stopped by Link's and Toon Link's Bomb, but not by Samus' own Super Missile. I'm not complaining about the latter, but the former should be eaten up like the latter. Ganondorf's f-air and Diddy Kong's side special, Pac-Man's side special, and Sheik's side special render Samus' Charge Shot useless. Also, Super Missile doesn't even kill. Sure, Samus is currently low mid-tier, and that's great, but if the developers could just make Samus a tad better would be great.
I hate Samus' limited CQC options. You'd think after the release of Metroid: Other M, which was released before Super Smash Bros. for the Wii U/3DS, would have given Samus a case for dealing with fast characters who get up in your face. I'm looking at you, Fox, Sheik, and Marth. F-smash still whiffs sometimes. Perhaps that hitbox could be a little bigger. Also, short characters are completely unaffected.