head to head
Neither is simply harder - they are hard in different places. Mystery Case Files: 13th Skull demands more variance; Portal demands more execution.

Optimization · Pure Optimization
A hidden-object adventure about searching scenes and solving fixed puzzles.

Optimization · Pure Optimization
The portal-gun puzzle game whose solutions are everything.
Mystery Case Files: 13th Skull leans Optimization (Pure Optimization); Portal leans Optimization (Pure Optimization).
Portal leans clearly harder on execution.
Mystery Case Files: 13th Skull
Pointing and clicking, no twitch demand
Portal
Portal placement timing modest.
Mystery Case Files: 13th Skull leans a little harder on reads, though the gap is small.
Mystery Case Files: 13th Skull
No adaptive opponent, puzzles are fixed
Portal
No adversary modeling player.
Mystery Case Files: 13th Skull leans clearly harder on variance.
Mystery Case Files: 13th Skull
Hidden-object locations unknown until searched
Portal
Deterministic chambers; no randomness.
Portal leans a little harder on optimization, though the gap is small.
Mystery Case Files: 13th Skull
Solving puzzles and finding objects is the whole loop
Portal
Pure puzzle-solving optimization.
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.