If you wish for a stronger, Tolkien-esque elf, then make them immune to natural diseases. This is a much stronger ability that can easily explain a near-infinite lifespan, but it is still more balanced than removing the -2 Con penalty outright, or even changing the penalty to another ability score. This would make an elven character as desireable as a 3.5e dwarf; a bit strong but not in danger of getting a level adjustment.
There was a time when I considered making my elves more Tolkienesque, but I ultimately decided that I'd like to keep them on par with my other core races (humans, dwarves, and half-elves). As for balancing ability scores, one subrace has -2 Strength, +2 Intelligence, +2 Charisma (since the half-orc gets the exact reverse and it is considered balanced, I think it should go the other way as well) and the other has -2 Int, +2 Dex.