Mercenaries hands down. Very fast-paced, action-packed, competitive, and tests and pushes the limits of your skills. And best of all it allows you to play as other characters aside from just Leon and Ada.
Separate Ways is alright, as it gives insight to the plot and let's us use a different weapon, the Gunpowder Crossbow and puts us in new areas in the same locations.
I'm not very fond of Assignment Ada, and found it to be more of a chore than anything else. The island is probably the more boring part of the game, we know the terrain already, and we have weapons that can't be upgraded or access to new ones, the plot behind it is also very dry and lacking and doesn't really make sense in my opinion, it just seems very redundant to me.