From a player's perspective, here's my thoughts. I have weakness in the hands due to cubital tunnel syndrome and possibly a little arthritis. My setup is *extremely* low-- clearance over the first fret from high E to low E is 0.009, 0.011, 0.013, 0.015, 0.017, and 0.019. My action at the 12th fret is like that of an electric-- 3/64" high E and 4/64 low E. The neck is almost dead flat with very little relief. I have a very light touch on the strings and prefer to let the microphone do the work for me. That said, this setup requires an almost perfect fret job and extra time setting the radius of the top of the saddle-- *NOT* removing material from the bottom of it to achieve. I also use stainless steel or nickel wound strings as they have a lower overall tension when tuned to pitch than most bronze strings. I don't necessarily believe that short vs long scale has a *great* effect, although the distances are certainly shorter with the short scale. Neck thickness from front to back makes a HUGE difference to me, and I prefer a super thin neck that does not get much thicker as you go up the neck towards the heel. Paradoxically, a wider nut may allow the fingers to relax more as opposed to curling up so much to fit a smaller nut width. As far as the frets, it's counterintuitive, I know, but I think lower, smaller, flatter frets will make playing easier as long as you don't do a lot of bending notes as on an electric. Lots of jazz players use frets almost "stoned into the board," so to speak, for that reason. My best advice-- get the action as low as possible and after the frets are installed, immediately do a fret leveling and dressing. Even brand new frets can have some high spots that require the action to be set higher to overcome. When I do a setup on one of my guitars, it is quite literally an all day event. Most luthiers may take a few hours at most... one I talked to at a now defunct local music store even bragged about being able to make a nut in less than an hour from start to finish. The nuts I make take about three hours and are dialed in to the thousandth of an inch. And-- this is critical-- when dealing with actions this low, be sure to set the action at the 12th fret by adjusting the TOP of the saddle *FIRST* before attempting to get the nut slots to final depth. Clearances this low ARE susceptible to a small amount of material removed at the saddle. On one of my instruments I have a "summer" saddle and a "winter" saddle. On another instrument I have 4 saddles I interchange depending upon how high action I can tolerate-- nut slot depths were set with the lowest saddle, incidentally.
I don't know if this helps as I am not really a luthier, but I do have very specific measurements I take great pains to achieve because it's the only way I can play comfortably. If I can help at all, please let me know!
John