My understanding is that UI lag is a consequence of holding all the UI information server-side so that Square Enix can more easily perform stress tests with it. For release, it, along with a number of other things, will be included client-side and speed interaction up quite a bit by release.

Mouse lag is a similar issue. Square Enix has already announced that a hardware mouse is programmed in (the third party tool merely enables it), which will also likely see client side activation at release.

Fatigue, as I understand it, has also proven to be something of a non-issue. That said, it was always a non-issue. Every developer decides a pace at which they want their players to progress. Inserting a cap is one way to do this, although an uncommon one.

As far as I can tell, the alternative is to add a rested exp. system. To keep the same rate of progression, though, Square Enix would likely introduce an exaggerated exp. curve: the same thing that FFXI gives such a negative reputation. I'd much rather have a fatigue system and be able to achieve more in less time than have a ridiculous exp. curve and spend double or triple the time grinding for the same rank progression.

The other things seem like minor gripes. If people really, really complain about them, they'll get added in. SE is difficult with their playerbase, but they're not stupid.