The troubles mainly have to do with the planning. The use of RC obviously is a bit complicated but one will get used to that over time. But when it comes to planning you are stuck with a cumbersome routine. In AFS2 as it is now you can create a plan with a few clicks and you're done. With AFS2RCATC you have to take a lot of steps to get similar results: find a plan online and copy it into a 3rd party planner (or create one in that planner), edit it, export it, load it into RC, somehow copy the plan into AFS2 (by manually creating something hopefully similar): all in all this isn't exactly hwo things usually are done in AFS2. With AFS2RC you need 5 programs to get things done (a browser, a planner, RC, AFS2RCATC and AFS2 itself) while with IPAC's ATC you will only need AFS2 itself.
The lacking features have to do with what IPACS's own ATC will offer, mainly AI traffic (making ATC useful) but also an in sim planner, weather, etc. so things that make the experience complete. Of course these things can't be expected from AFS2RCATC which I why I also added "which isn't Aerofly FS2 RC ATC's fault btw". So nice as AFS2RCATC can be it is limited compared to what IPACS's ATC will offer. (Whenever (and if ever) that may happen, of course.