Then paint the soffit, cabinets and trim a nice white.

I'm asking what you would do, like...Update the cabinets?

In the context of your apartment building search, functional obsolescence may include not having W/D hook-ups (and no laundry building), no central A/C (only window units), no dishwasher, limited kitchen (e.g. 2 cabinets, limited countertop), 3 bedroom 1 bathroom, 7' wide bedrooms, no electric ground, ... in otherwords 'things' you wouldn't ever see in anything built recently.

Every 8 years, replace all faucets, under cabinet water lines,  toilet mechanicals, washer and dryer lines and vent hose just to name a few.    

The kitchen cabinets are dated, but hardware, and or/paint and hardware can make a major difference in the way they look.

The scope of work on this potential deal will be cosmetic and systems - such as interior & exterior paint, new plumbing, electrical, kitchen cabinets, some windows, refinishing wood floors and maaaaaybe a new roof.

I'm not sure how to handle negotiations with him.2) To complicate matters, before he moved in I tore out the kitchen cabinets and installed brand new cabinets and brand new granite counters.

It mostly needs updates (flooring, paint, kitchen cabinets), no major rehab. 

He is also a cabinet guy so I think i'll be offering him the opportunity to finish some work on the house too...he did build out the kitchen himself, used to work for my father in law, and does good work.

Such as cabinets size and quality, Granite selection, etc. 2.