When buying a boat, let the seller make repairs. Rather than have a seller discount a boat because of needed repairs, have them fix it using a reputable repair service. It's almost always more expensive than you — or they — think.
Not all upgrades will increase the market value of the vessel. In many cases, what a boat owner thinks is an upgrade that will increase value is normal maintenance. For example, if a boat owner rewires his boat, that's not necessarily an upgrade that will increase value; it is maintenance that will keep the boat current with standards and safety concerns.
Coast Guard regulations don't cover most parts of a boat. Boats have to be built to U.S. Coast Guard standards, but those standards cover only a few things, such as fuel and electrical systems and marine heads. ABYC standards cover many more things. While boats don't have to be built to meet them, yours should be.
The 'lightly used' theory. If a boat has been sitting for two or three years, it almost always will need more work than you think. Boats and engines last longer when they're regularly used, and problems compound when they're idle for long stretches.
Sellers don't always have to disclose problems. Other than a known defect or condition that might render the boat or engine unsafe, there is no obligation for the seller to volunteer information the buyer does not ask for when buying a boat from a private party. Ask the seller if there has been any major damage repaired from collisions or sinking. Use buyer/seller forms and note what the seller says before you and they sign it.