Order in menu

Spells would be relatively easy -- just move the data around in usME. It'll take some time, but it's pretty straightforward. Similarly for espers -- move the data into alphabetical order -- except you'll also need to do some event editing so that events which give you espers still give you the right ones.

Characters are more complicated, because you can rename them (unless you're taking that function out of your hack?) -- you can't just reorder the data (which would be a massive undertaking ANYWAY, as you'd have to alter every single reference to every character in every event that references a character), because you don't know what alphabetical order is going to be. That would definitely require more extensive menu hacking, especially as, so far as I know, those currently work based off of character ID.

ETA: Oh, and for spells, that's with the caveat that they'd only be alphabetical based on the default sorting; if someone changes the spell order in config, that goes right out the window. But you could always disable that menu option?