As many have suggested, radiant floor heat is a MUST! I don't know where you heard that you'll lose heat to the ground, but if the slab has been constructed and insulated properly, it won't happen. Radiant floor heating makes having a high ceiling practical.
Separate, sound insulated room for you air compressor with sound attenuated venting to the outside. If you can, make it big enough for a dust collection system in case you decide to expand into wood working.
Lift/hoist... Well, the garage I work in has a huge beam spannign the width and is equiped with a chain hoist we never use. When time came to pull an engine, I used an engine crane (get a folding model, btw). I long for a 2-post lift. At the moment, I have seven cars to keep track of. I would probably use a lift at least once a week.
High ceiling. You can't have a high enough ceiling. Especially if you get a lift. Cooling in the Summer will be easier. As for heat, see comment #1.
Put EVERYTHING on wheels or hang from the wall. Shelves, cabinete, benches, everything. This makes cleaning much easier. Hang work benches from the wall so they keep the floor clear. Personally, I'm not a big fan of a large workbench. Flat surfaces collect crap.
Polished vs. epoxy. Well, there are benefits to both. Both require regular cleaning and care. Epoxy has one big benefit, IMO: it is a much brighter finish and therefore makes your lighting much more effective.
Air plumbing, receptacles, etc, have been gone over.
Unfortunately for me, I work in an industry where I design electrical systems for high-end cGMP facilities, so I get all sorts of engineering ideas that easily apply to garages and so I'm dreaming about this sort of thing constantly. However, cGMP facilities are not cheap. /ubbthreads/images/graemlins/crazy.gif