From what I can see (and this is based entirely on gameplay videos and not actual experience), one of the big things that is not in WotS, but I "think" is a major feature of TF:A is flight deck management.
In WotS what I'm seeing so far is that you buy your planes, and then just launch your strike. In TF:A, I think a lot of the tension is compiling your strike package while simultaneously managing your CAPs and cycling aircraft through the flight deck. It's that tension of when to bring planes on board vs. keeping aloft a bit longer at the risk of losing them, or deciding to shoot a partial strike or wait until you can get a complete coordinated package together, that make the carrier battles so interesting. I don't think this is present in WotS.
I'm sure there are many other aspects. I get the sense that TF:A is a more granular carrier experience.