ED and APD play very differently to each other as well, so replaying as the other side will force a change in playstyle (unless you're just looting hostile gear).
The eurasian diarchy has very different weapon styles to the APD....the archura launcher cuts through armor and shields like a knife through butter, but it fails epically against hardened targets that require WMD. Their heavy energy weapons share this general theme...very high damage, relatively low rate of fire, and trading great armor/shield damage for a lack of WMD (which, again, does not make them good station busters or capship killers). If you've got a way to deal WMD and just want to be able to crack armor.....the ED equipment is very very good. I have not tested their stealth armor yet, but the statistics on it are significantly better than the (rather horrible) D&O stealth armor. Their endgame gun, from memory, is a positron cannon of some sort. I haven't tested it though. The APD on the other hand goes for WMD, and lots of it. Their Xianwu-700 howitzer is the best of the three large nuclear howitzers (beating the hecates by 1 average damage per shot, for the same poweruse and fire-rate, so it's not THAT much better...except you can hack them off stations for free), and their endgame weapon is an absurdly good (although not as pretty as I'd like) plasma cannon that accepts both high-speed loading (IIRC) and optimisation ROMs, becoming what I currently consider to be one of the best weapons in the entire game. Plus "Space Command" is an awesome name for an organisation. It may be the case that I favor APD a
little over the ED.
Personally I have not done any significant missions for the NAU (or rather, their ATLAS intelligence branch), even though I'm a member.....they offered I think one or two rather simple things, then never offered anything else. And the UAS missions seemed to cut off after a while as well, although this may be because of my joining Space Command. They pay well in the early game though.
EP could definitely use some post-endgame challenges (helping lillith gain control of more nodes, etc), and a bit more signposting....but I've liked the mission path I've taken in my completed game. Mostly because the APD does have some
very nice guns. Their missiles are a bit odd though...they don't seem to match their descriptions.
) . I then got the mission to take Lilith and kill a Dreaming Stronghold. Fair enough. Blow up Stronghold, run off. At this point I gate out but can't find Lilith or Morningstar anywhere. I've checked the Ranx Empire, the Ungoverned Territories, and Eternity Port itself. I've got no Quest, and about the only thing I haven't done is go poke around the Near Stars. 
