In my opinion their naval capacity was terrible in both SC1 and 2. For a start, only three Aeon naval units possess some kind of anti-air capabilities and there aren't any torpedoes either apart from the submarines. However their capacity in land battles is more favourable if you can get a Colossus walking. Then again it doesn't have anything against aircraft or submarines.
And in SC2 they didn't even have a navy. So apart from certain aspects I stay away from using that particular faction.