Generally, although it had some insanely stupid parts, I prefered Far Cry overall.
Half Life 2, though superbly presented, seemed nothing more than an arcade game ported to the pc. Even though it will soon be the other way around. The design is perfectly linear for an arcade shooter. It wouldn't surprise me if they added a countdown for when you reach the ever present physics puzzles. Speaking of which, they were so setup as to be purely unrealistic.
Freedom to make choices (ie. interactivity) is what games are all about. Half Life didn't have this IMO. I think merging the 2 design styles would be incredibly difficult though. If they spend a lot of time getting one area of scripted stuff to look good, you don't even know if the player will see it. With the rising costs of development, this could be too expensive for what it's worth to the player.
I agree on the balance of Half Life though. If Far Cry had quick saves and a better ending (after getting through the terribly hard ending you are presented with a "boss" that you shoot once to trigger the last cutscene) it would have been game of the year.
Boy that was badly written...