I suppose part of the reason lies with the fact that since the Enclave is your primary enemy in Fallout 3, they didn't want you to have the ability to loot an amazing state-of the art only-armor-you'll-ever-need power armor from every Enclave soldier you kill.
If thats the case though, why not just make most of the armor on the soldiers non-playable? With only one or two locations where you could get the APA? Hell it would also mean that Enclave troops would be stronger.
Oh Bethesda. :sadvaultboy: