one of the things I think Guild Wars II did correctly was their pvp. every week 3 different servers would fight. so instead of pvp zones of heroes against villains I think i would make a zone of servers against servers. so every week you would have two new opponents to battle. new being relative as you would end up fighting at least one of them again a month or so later (because of the limited number of servers).
kind of a marvel vs DC vs dark horse thing where only one universe can win or the multiverse will be destroyed.
i would spend a lot of love on Bases making things useful.
I spent years on my base. it was a solo thing but I was darn proud of it. second largest map, bowling alley, movie theater, flight deck, library, stadium, operations center, hospital, arboretum, teleport room, and SG housing. but i digress.
I would add a feature to the game where you could edit and make items for the base. once made they would be submitted to the dev's and if approved they would show up in the base editor for anyone to use. new wall panels, statues, kitchen appliances etc.
I would also add a size scroll bar for all base items. be able to change the size of everything including stretching.
change the location of your base entrances. keep the default in the same area, but if you want you can change the base entrance in each zone. Top of the globe, warehouse, make it show up on the map for SG members, and glow / stand out so it can be seen by SG and team members only.
make more items that would be useful
raise the storage for salvage up to 100. 30 was way too low.
Names.
I like the idea of names that several people came up with so you could have multiple names on the same server. my only change would be something that would say "there are 336 other people with that name"
Characters/costumes
Moving lips...
Symbols on capes. (SG and otherwise)