Latios has higher offenses than latias, but only by a few points each. Choose latios if you want that extra bit of power: plus his moves are more attack oriented.
Latias-Tons of helping moves like refresh, safeguard, helping hand, and healing wish. (granted, latios can still learn these as well.)
Latios-Power based attacks like dragon dance, and dragon pulse,
Their movesets are pretty similar though.