Yeah, WWX has been designed to work normally after the campaign.
As for cramming in many mods, Rebirth is quite good for that. I only mention those two mods since they are big mods that change game play quite a bit and at the moment, they are not compatible. First Person Gameplay Overhaul mod and BettyAI 2015 are also quite big not sure if that creates any problems or not.
Pretty much most other mod can work with each other without worrying about install order. There may be exceptions but if you stick with mods known to be working with the latest game version (or others that are relatively recent and don't have issues reported in their threads) and check mod threads in case of reported incompatibilities, you should be ok to go mental.
Full list of mods known about to users of the English modding forum:
http://forum.egosoft.com/viewtopic.php?t=370788
There are quite a few more on Steam Workshop but to get ideas about them, you'd need to make a judgement based on the date of last update and Workshop comments.
As for recommendation, I personally find the following finished mods offer abilities I enjoy:
Miscellaneous OOZ Combat Tweaks (there's an IZ option too)
Carrier & MoreCarriers (lets Fighters dock on carrier)
MultiAssignment (cuts down on the time faffing about with chatting NPCs)
Galaxy Station Range (for ships assigned to your stations)
MitchTech Station Logistics (X3 CLS-like option)
Auto Trader / Yet Another Trader (X3 UT-like options)
5km Scan Range (makes activating infopoints on station after station less annoying)
Capital Ship Bridge (epic)
Orange Mouse Cursor (altered contrast vs background)
Sidebar Extension (used by some mods)
Trade Menu Cargo Hold Filter (makes the Trade Window a bit more intelligent)
OOZ ship build (saves running around the galaxy for shopping)
Mission Computer (a bit like the old bulletin boards)
Slightly More Useful Plot Station (in case you'd like a plot station to make some ship components)
Station Engineers (player stations repair over time)
There are many other great mods, with some under development, so don't take the above list be restricting
Edit: Typo in last sentence.