For the flak there is not much difference. Between UEF and Aeon mob shields, the Aeon one hovers and I believe has more shield points (about 1000 more) than the UEF.
(Aeon 5000 shield UEF 4000 shield? I think? Horrible feeling I am wrong here, someone correct me)
Also the UEF has slightly more hp but that doesn't really matter.
Aeon costs slight bit more energy a sec to run