Aight, no april fools, serious business.
__
In theory, I say marth is doc's hardest matchup.
Marth's biggest strength (zoning) is doc's biggest flaw. Marth is faster than doc, and he can handle pills in every way you're supposed to (he can zone against them, and he can run from them). Although Doc can gimp marth, Marth can gimp doc just as well. More of a problem to doc is that marth can actually defend himself well while recovering.
For me personally, I say Capfal is doc's hardest matchup.
Capfal, by generalization, is a rushdown character. The best way to stop rushdown is zoning (or evasion if you're faster than said rushdown character). Capfal is the fastest character in the game and has the biggest jumparc. Doc's zoning is his flaw. Do the math. XD
It also doesnt help that Capfal flatout has more range than doc (save pills), so zoning is really a 1 shot effort. The one thing Doc has on capfal in this matchup that he doesnt have on marth is that Doc can chaingrab Capfal, and gimps him easier (because of capfals recover, and because it's hard(er) for capfal to defend himself). That's why, as much as I personally ***** and moan, i know it's not the worse.
In the grand scheme of things, I say you realistically can put Marth, Capfal, and Sheik in a hat, draw them out at random, and those are your hardest matchups.
___