Both are very different games, and both are excellent. Even though it's sufficiently open for different tactical approaches, FC1 is more straightforward in terms of storytelling, progress and exploration. You keep pushing forwards to new areas and chapters. In FC2, you have one wide map, accessible from the beginning, and missions popping up here and there, so it's more quest-driven while FC1 is more like a traditional shooter.
I might marginally like FC1 better, for the green-and-blue setting and its refreshing feel of freedom whin you dive from a cliff to a very blue transparent sea. FC2 is more yellow-and-brown, having you swim through muddy rivers and run through dry bushes. FC1 is more basic fun, but it's plagues by mutant creatures after a certain while, while I prefer sneaking around humans with human abilities.
Generally speaking, I really can't relate these two games. Their styles and gameplay are too different. They should be played both, just like one would play both Borderlands and NOLF. Don't approach them with the same line of questionning as "should I play thief 1 or 2" or "hitman 2 or 3", because these two Far CRy games really don't feel like belonging to the same series.