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well, actually, aggron has less weaknesses than metagross. metagross has stronger defense and attacks. but it really depends on who u need. if u need a tank, choose metagross (i would choose donphan), but if u need a pseudohazer (someone who knows roar or whirlwind), then i would use aggron to withstand the attacks. metagross does have meteor mash though...
Aggron gets taken down by water attacks super-easy, and there are a lot more pokemon using water attacks than any other attack. Metagross, though he has his weaknesses, none of them are as glaring when compared to Aggron's vulnerability to water. So my suggestion is Metagross (and it's the correct suggestion, since my name is....)
It does depend on the rest of the team and who you like but for me I like Metagross because it learns Hyper Beam, Psychic, Meteor Mash and it can learn good TM's. So can Aggron though...Also in the Ruby/Sapphire Player's Guide it says Aggron is strong against 10 types and weak against 3 and Metagross is strong against 9 and weak against 2...I don't know who is better but I like Metagross even though I've always had Aggron in my team.