Repaint or replace.

He did NOT prime the whole surface first before painting, or use a combo paint-and-primer-in-one product, like Behr.This was for a complete repaint INSIDE AND OUT for a house I’m selling, not renting, and the paint was NOT going over bare drywall (or a flat sheen covering a high gloss sheen); it was simply a color change between similar colors and sheens.The bid he provided did NOT include the words “prime” or “primer” anywhere, but I thought my instructions and expectations were clear, and I assumed where the bid said “paint” that it would be a paint-and-primer combo product.

If no more leaks, and the ceiling drywall is solid, and not spongy, weak, or wet feeling I would just prime with oil stain blocking primer and repaint.

Hi Josh,If you're going to do this, you'll need to find the leak and fix it before fixing the ceiling.If it's wet up there beware of electricity too.The ceiling can be a homeowner fix (how well it's done is up to you and your skill).If you choose to try it, you'll will need to match the drywall texture, and prime the fix and entire discolored area with primer that covers water spots, and repaint the area to match (or the whole ceiling).If the drywall is heavily damaged that will need to be replaced too.The sell texture repair spray to help with this (see YouTube for how to use it).Good Luck!

Repaint at least a couple of rooms with more modern colors.

@Graham NadlerVinyl floor, no garbage disposals, a paint color that can be used as "touch up" (i.e. without having to repaint the entire wall), pex pipe, a working fan in the bathroom, leave a few furnace filters behind for either yourself or the tenant to change, no screens unless lease says tenant will maintain repairs, bathtub surrounds that use very little to no caulk (reduces mold).

I'm not sure how costly it's going to be to repair and repaint.

Just by the things you’ve said you could be within your rights to charge for repainting and fixing the hardwood floors.  

We updated all the appliances, renovated a bathroom, added new landscaping, repainted the interior, added new floors and carpet throughout the house, added a paved patio in the backyard, and replaced the A/C unit.

You'll have drywall cracks, so you should factor in drywall repairs and repainting. $$$4.