Maybe you did not use it correctly then as I do what you describe with it perfectly fine?
It's basically nothing else than Alpha gear if you just use the General section and add your different sets + skills to use.
It's even easier than AG2 to add the skills by using SHIFT + click etc. (the tooltips show you that info).
Everyhting else is the same: Drag & drop skills / set items.
Like this screeshot here shows (even looks similar to AG2):
Just define your 2 skill bars, define your equipped items at the icons at the topright of each row and even define your champion points etc. at the bottom right of each row.
You change those setups manually via keybinds then e.g.
This is nothing about optimization, it's pretty the same as AG2 does.
Edit:
Not sure about the "1 skill changes", if this is easily doable with those "General" setups too. Maybe it only works within trials/dungeons then.
But I'd simply ask the author for it, if there is already/or if he is willing to add a way to make it work with those profiles too.
Perhaps someone here reading this knows a better way or another addon but I was not able to find any. And I bet noone is interested into creating the next addon doing all that, reinventing the wheel, if there would be a cleaner and easier solution: Use an existing addon, modify it to add that feature if possible.
Creating addons, especially skill and gear related ones, can take months to accomplish and make compatible with all other addons and game code (espeically the testing is a big time invest!).