But those are still available, you just can't shortcut them, so those are not actual tradeoffs.
Well, it's one reason you'll have to learn inputs if you want to compete.
Another reason is that if you only use combo assist you can no longer do Opener directly into a Linker, it will always be an auto-double. You want to make yourself more predictable and easier to read then I'm sure nobody will complain. If you want to keep your opponent guessing by mixing in a few Linkers following an Opener you'll have to learn the special input.
I imagine some people are going to substitute combo assist moves into their combos, but not use them entirely if they plan on sticking with the game to compete online.