I have just replaced an 2004 Yamaha 4 cycle 25hp on a 13ft Boston Whaler with a Suzuki 25hp. In researching this I got some surprising input. The Yamaha 2 cycle were legendary for their reliability (and still are if you can buy one a 2 cycle outside the US where they are still sold). But I never liked my Yamaha 4 cycle. It was really loud and rough. And the carburetor was very, very sensitive to ethanol fuel fouling. I was always in the shop having its carburetor cleaned in an ultrasonic bath. In New England it's almost impossible to find ethanol free fuel.
That said, the Yamaha's are still really popular and their marketing is great. But I concluded that Yamaha, Suzuki, and Honda are all great engines and depending on the model, one can be better than the other. At 25hp, I concluded Suzuki has a better offering at the moment.
The other good news is that more and more outboards are fuel injected rather than carbureted. The fuel injected outboards are reportedly much less prone to ethanol problems. All the 25hp's are now fuel injected. But at the smaller HP many still have carburetors. I would try to find an outboard with fuel injection if you live in an area with ethanol fuel.
To your other question. Remote controls are a big plus. If the outboard is located in a place where it's easy to pull the cord, the electric start is less important. As others have said, be sure to find one that takes a prop pitched low for a heavy keelboat. Also the largest blade size you can get. 4 blade if possible.
To your recent problems. If the engine has ever seen ethanol fuel, consider replacing the carburetor. It may have an accumulated varnish that no regular carb cleaner will get. Clean out the tank (get it dry) and fill with fresh fuel. Replace the spark plugs. Replace the little fuel filter inside the engine. If you still have problems, replace the fuel hose from the tank. For reasons I don't understand, they often are the source of outboard starting problems.
