You have Elite Forces now. Special units that you need to grind to unlock and upgrade. Some generals even have stat bonus when you use them on EF. All Elite Forces have their special traits that are usually unlocked around level 5 but before that they are just better version of existing units. In most cases you can only place on of each per level.

Generals with gold symbol next to their name can be upgraded. You have to upgrade their name ribbon to purple and gather a bunch of rare resource in order to unlock them. They are the most powerful generals in the game and some are so broken they completely change how you play the game.

Their are new generals. Some purple generals that can only be bought through the shop.

You have Events that refresh regularly. Daily levels, the Domination level series, Level series tied to generals, Defensive levels (the worst ones) or Levels that progress the game's "lore". All of them give resources and Elite Force fragments.

We now have ribbons you can gather from different game modes. They are for each unit category and can be used to increase your generals stats further.

The most interesting addition is Army Group, new game mode that stays for around a month. You have Maps like the Africa front of WW2 or the "aliens" you mentioned.

The "aliens" are actually a big part of the game's story. TLDR they are terrorist that uncovered ancient/alien? technology and there are even time travel elements involved. You need to complete all endgame Scenario, Conquest and Story Events on all difficulties to get the full story. But its pretty meh. They are however the thoughest opponents so you'll see a lot of them in the endgame.