Lower end of high tier, ie 16-20. I've tried convincing myself he's higher high tier or upper mid tier at varying times, but he's so unusual of a character that it's really unclear where he stands.
His worst MU is likely Ryu, because MK lacks the range and projectile that are essential for walling Ryu out, and his slow ledge options, low weight, and high falling speed leave him at the mercy of Ryu's combos and KO set-ups. He takes a clean 25-30% off a single conversion and dies below 80% to Shoryuken, giving him very little room for error. Ryu lives longer due to his own weight and MK's KO'ing set-ups being less reliable, though MK can get hard punishes with SL, up smash, and bair if Ryu over-relies on FA to get out of disadvantage. 60-40 in Ryu's favor. Thankfully Ryu isn't very common. Other losing MU's are Mario (results-wise; theory-wise it could be even), Sheik (slight loss), Sonic (may be even; Sonic is just annoying in general so that def affects views on the MU), Cloud (slight loss, at best even).
Among the relevant cast, his best MU is Rosalina by a long-shot. Other winning MU's among relevant characters are Pikachu, Villager, Ness, and arguably ZSS.
Problem with MK is that, while his reward is still quite good when he does get in, with up air (one of his most important moves) doing 1% less and comboing less effectively, and with his poor damage-per-hit, and vulnerability to trades, combos, ledge coverage, and zoning, MK requires too much effort and patience for not enough reward. Tyrant, Abadango, Leo, Jband, Seibrik, Katakiri, Technology, Demitus, among others, have either gone to co-main him with other characters like Sheik (Tyrant), or have downgraded him to a CP for specific MU's (Abadango). The only notable who's still almost exclusively using MK is Ito, and he's thankfully doing his best to reap the most of MK's conversions, and I really hope he can get some big wins at EVO while going mostly MK.
Edit: MK doesn't have a character who gate-keeps him, but going to a tourney knowing that you're going to be fighting multiple slightly losing MU's frequently puts a lot of pressure on you, and makes playing him in bracket mentally taxing.