I'm pretty sure it's not an issue. I just dislike it compared to the Steam version.
There is no "Quit" button (I can get around that, though), the pop-ups are slower in battle, and the little arrow beside the magic name that indicated the "All" property from the All Materia ("Bio >" for exemple), was easier for me to notice/process than the "All" in the bottom-right corner of the battle menu.
The menu without the enhancements just seems crispier and more practical for me.
Sorry I'm repeating myself, but I'm actually considering either abandoning the game or playing the game without the mod (which is a shame because the fan translation is great). I really can't stand the menu enhancement mod. I feel like I am obligated to NOT speed up the ATB in the settings, because if I do, I'm putting myself on disadvantage because of how slow the menu is. I even had a Chocobo run from me before I could navigate through the menu to pick the greens.
But then, if I leave the default speed on, I start dreading every combat encounter because of how slow it feels.
1.
On the lack of a quit button: Press alt+f4. I believe the removal of 'quit' is merely a limitation of current FF7 modding.
2.
On slower menus/pop-ups: I did some testing between R05c and *just* 60 fps by itself. In terms of speed, the only difference is that
R05c Menu takes a fraction of a second longer to load menus/pop-ups (before they become usable/back-out-able). This affects battle menus, the main pause menu, and possibly others. To see this yourself, try repeatedly going in and out of menus as fast as possible, with and without Menu installed. I can see how this could be a big issue with fast, hectic battles.
This should definitely be addressed in R06 if it isn't already. EDIT: eh, it's not
that big of a deal. Judge for yourselves.
...But personally FF7 is such an easy game that I haven't had any menu-related issues in my ~12 hours of play at %80 battle speed and 'recommended' ATB. Maybe that's why no one has noticed or brought it up until now?
3.
On the lack of a red 'All' indicator arrow: I totally didn't notice it was gone, but now that I do, I miss it. The 'all' indicator was objectively useful by allowing you to get more info at a glance, and I don't understand the rational behind removing it. There should at least be an option to keep it.
4.
On a Chocobo running away because the menus were too slow: Change ATB to Wait while you catch a Chocobo and then when you're done, switch it back. This isn't too much of a hassle, is it?
Best bet is to wait for R06. IIRC, the 60FPS mod has been reworked for the upcoming version. It should provide smoother menu use.
The slower R05c menus have nothing to do with 60FPS, believe it or not. It's all the Menu modifications. I just did the same testing as above, but minus 60 fps for both R05c and unmodded to the same results.