I don't know what you're talking about when you say that Mewtwo's U-Smash doesn't link correctly. The first strike only knocks opponents out if you just barely graze them. If it doesn't link correctly, then you probably deserved it. Believe me, I've had it happen to me, and it's really not that hard to avoid. You just have to time it right.
Samus's Up Special is also a fairly bad recovery move. Sure, Screw Attack excels at KO'ing, but it's a really telegraphed recovery move because it's her only option, provided she isn't within tethering range. Teleport excels at recovery, not KO'ing. It's hardly fair to compare them. And I don't think one good KO move can compare to KO projectile, a command grab that doubles as a reflector, and a powerful punish tool, especially when said KO move is a poor recovery option. Of course, I wouldn't say Samus's other Special Moves are as bad as you seem to think, especially Charge Shot. Sure, it's inferior to Shadow Ball, but that doesn't mean it's bad.
I'd also say that Mewtwo's aerials are better than you seem to think. His D-Air is quick for a meteor smash of its power, and it can KO without spiking opponents. Mewtwo's B-Air and U-Air have strange hitboxes, true, but his U-Air is a mediocre juggle move, while his B-Air covers a broad range and can create a "wall of pain" at certain percentages. Plus, you can use both his B-Air and U-Air to hit opponents through the lip of thin stages. It's a good way to knock your opponent away from the ledge as you recover. Granted, Mewtwo's B-Air has quite a bit of startup, but, once you get the hang of it, it's a pretty useful move.
Mewtwo's F-Air also has a misleading animation, but it combos into itself and low percentages and KO's at high percentages. Plus, it comes out very quickly for a move of its power level. Depending on the situation, it can be effective edge-guarding move thank to its high, horizontal knockback. His N-Air has a large hitbox and traps opponents with auto-link angles, which deals decent damage. Plus, going off what @
pikazz
says, Mewtwo's N-Air true combos into any aerial, barring his D-Air, at specific percentages. Also, similarly to Mewtwo's B-Air and U-Air, when recovering, you can use a rising N-Air to catch opponents sitting at the edge of the stage, which is facilitated by his N-Air's lingering hitbox, though the opponent must be closer to the ledge than with Mewtwo's U-Air and B-Air.
One matchup doesn't define a character. Besides, the Mewtwo/Sheik matchup really isn't too bad. Sheik may be able to rack up damage, but she has problems KO'ing Mewtwo, and Needle can be reflected. Plus, Shadow Ball overpowers Needle, and Sheik is pretty light. The matchup is difficult, but it's not totally in Sheik's favor. If you play defensively, keep Shadow Ball partially charged at all times, and watch out for Bouncing Fish, you should be fine.
Considering that, according to
the latest community tier list, Mewtwo ranks 6 spots above Samus, I'd say you're likely either overrating Samus or underrating Mewtwo. Neither of them of are great, but neither are terrible, either. As a far as tier lists go, they're both pretty average.
EDIT: I edited out the stuff about Teleport ledge-cancelling. I was misinformed. My apologies. I also lack the ability to grammaticize today. >_<