Input complexity is a design decision with a plethora of balance decisions put into it, but all that means is if you opt for input simplicity you have to make other balance decisions to rectify the difference.

Rising Thunder gave the special moves cooldowns, so you couldn't spam Guile Flash Kick and still have to use normals.

Granblue Fantasy did the same thing except they also had the complex inputs which would have shorter cooldowns if you used those vs the simple inputs. So if you used Guile Flash Kick the simple way you would not have it up as fast and need to use normals longer.

Fantasy Strike doesn't use cooldowns and instead adds other negatives, typically worse frame data than usual but to continue the Guile example, FS has a Guile character in Geiger, who they balanced out by giving him a Gear meter that is used for his Sonic Boom & Flash Kick, and is used up enough between either that you're losing temporary access to one if you do the other. So if you Sonic Boom you can't Flash Kick to stop them jumping over your projectile right away if they're close.

For the most part the main thing you actually have to watch out for in simple inputs is command grabs, the 360/720 input is built around forcing players to either chicken wing it out as a reverse counter on standing block, do 632147 while dashing, tick SPD it out, etc. The input is specifically designed to be near impossible to pull off on a whim.

Just means they need to have their damage & frame data adjusted to account for that though, or again tied into a meter to make them not spammable.