You can right click on the ability and toggle autocast on/off en masse, but that usually won't help with activating the ability unless you have a convenient autocast...

Well, there are very few abilities you'd actually want to do this on anyway, but for the few it would affect it obviously is a huge drawback being unable to do it quickly...the main ones I can think of are the self-repair on the skirmishers and enforcers as well as the kanrak/sentinel abilities...martyrdom and repulsion might also be worth looking into...the last group would be anti-SC abilities like flak burst, TK push, and JW, but tabbing is somewhat viable with those depending on what caps you have and what order they appear in the empire tree...

You could mod the ability files so that the skirmisher/enforcer self-repair abilities autocast at a higher hull %, that would be a fairly simple mod, only editing 2 files...idk about charged missiles, might not be able to tweak those...were there any other abilities you were interested in?

illum copies

I have not clue how to mod the files, but yes the ones you mentioned is pretty much the most important ones that I could think of as well. I am uncertain when repair stations start to repair, but could the same thing be modded for buildings as well? 

Though I suspect the main issue is that ones you have modded your game, with even such a small thing as earlier ability triggers, you are left with multiplayer issues. Not being able to join other peoples games, because of different game files.