FAL:
Pros-cheap mags...sometimes as cheap as $5 each. Cheap and readily available spare parts and accessories. Many good manufacturers to choose from, and even the low-end parts guns can be improved to an acceptable quality by a good FALsmith for not that much money. Very ergonomic (at least if you get a light-barrelled one), very reliable, good combat accuracy (groups aren't as tight as a comparable M1A but I can sit out at 150 yards or so and toss aluminum cans in the air with iron sights). I prefer battle rifles with a pistol grip, YMMV. Field strips more easily than any other combat rifle I've ever seen, very simple to disassemble and reassemble. Has a bolt release catch.
Cons-Most scope mounts are not very stable due to mounting on the dust cover. Heavier than the M1A. Iron sights are not optimal, although I think they are good enough for combat. Trigger pull is a bit heavy. Prebans are very expensive.
M1A:
Pros-Very accurate and reliable, well-balanced and fairly ergonomic. Lighter than most FALs. The best iron sights on any combat rifle made IMHO. Mounts a scope fairly solidly. Trigger pull is very nice. You can have a flash supressor on a postban, and you can buy a preban without breaking the bank.
Cons-Very complicated to break down, especially if you take out the op rod. Mags are much more expensive than FAL mags---usually $32-40 for used, $50 for new. Accessories are a bit more expensive than FALs. Doesn't have a bolt release catch, so M1 thumb is a danger. Doesn't have a pistol grip, but that is a personal thing, YMMV. Newer M1As use more cast parts than older ones, so you have to watch that.
Basically, it depends on which rifle feels best to you. I have both and I like the FAL better, but I also think the M1A is a fine gun.