head to head
Neither is meaningfully harder - they pose close to the same test. The widest gap is execution, and it is a single point.

Execution · Competitive PvP
High-speed tag-team execution and human prediction in gleeful early-Versus chaos.

Execution · Competitive PvP
Classic fighting execution and human prediction atop a famously unbalanced roster.
Marvel vs. Capcom: Clash of Super Heroes leans Execution (Competitive PvP); Mortal Kombat Trilogy leans Execution (Competitive PvP).
Marvel vs. Capcom: Clash of Super Heroes leans a little harder on execution, though the gap is small.
Marvel vs. Capcom: Clash of Super Heroes
Chain combos, assists and infinites demand fast precise hands
Mortal Kombat Trilogy
Dial-a-combo inputs and run-meter pressure demand fast hands
Marvel vs. Capcom: Clash of Super Heroes leans a little harder on reads, though the gap is small.
Marvel vs. Capcom: Clash of Super Heroes
Baiting a human's assist call or super is the duel
Mortal Kombat Trilogy
Human opponents must be baited into unsafe moves
Same score on variance - which means the number cannot separate them. The difference is in what each one asks of you.
Marvel vs. Capcom: Clash of Super Heroes
Hidden characters aside, everything is public
Mortal Kombat Trilogy
Movesets are public; nothing hidden in a match
Same score on optimization - which means the number cannot separate them. The difference is in what each one asks of you.
Marvel vs. Capcom: Clash of Super Heroes
Team composition and infinite-combo knowledge define the meta
Mortal Kombat Trilogy
Knowing the bloated roster's broken tech is half the battle
A matching score does not mean a matching test. Two games can both sit at 10 on execution and demand completely different things of you - which is why the reasoning above matters more than the number beside it.