Gas or Diesel
If well looked after there will be no more problems with one or the other. If left to rot both will bite you.
Dirty gas will plug a filter, as will diesel. Water in the fuel will cause a gas engine to quit, repairable with some methanol and perhaps draining the float bowl. If water get's past the filtering system of a diesel it will destroy the pump, and most likely blow the tips off the injectors since the pressure required to atomize diesel fuel (about 14,000 psi) is enough to cause severe mechanical damage to the system trying to force the relatively high surface tension of water through holes that are almost too small to see. Here again the cost issue comes out. A carburetter and distributor rebuild (which you can most likely do yourself) is really cheap compared to a diesel injection pump/ injector rebuild/exchange. Also diesel fuel and everything it touches stinks. Moreover diesel fuel will grow a filter plugging organism extremely quickly if conditions are right rendering the fuel and all components of the system useless.
That being said, diesel, with a clean fuel system and semi regular oil changes will cause very few problems, and clatter away for a long, long time.
The higher BMEP (Brake mean effective pressure) of a diesel, combined with the higher calorific value of the fuel, and more importantly the fact that diesel fuel will burn in the cyl. no matter how little of it is injected mean better potential economy. Gasoline needs to be mixed with air at a very specific ratio, (called the stoiocheometric ratio, about 15:1 air/fuel by mass) in order to burn. Generally primative carburation systems lean toward the rich side in order to assure combustion and to keep the threat of detonation low at all throttle settings. Diesel injects a specific metered amout of fuel each cycle, dictated by the the RPM the governor is set to achieve. (If the engine cannot achieve the RPM that the governor is set at because of loading then the pump will run at full rack, injecting as much fuel each cycle as the the pump is able whether or not the engine can burn it competely or not, passing the unburned fuel out the exhaust as black smoke/soot. The point being that if operated below the tourque peak a diesel will always be more efficient than gasoline. I'm not sure if fuel savings alone would ever equal the much higher initial cost or rebuild cost. Diesels are, of neccessity built more robustly and hence can expect a long life. The Atomic 4 was designed with very low component loadings so it too can expect a long life.
Treat the fuel system for gasoline with the same respect that you would treat a pressurised propane system. Use the best quality components on every joint and fitting and check them annually or better. No fumes, no boom!
As far as an outboard is concerned, they can be a pain. They put weight where it doesn't belong. Without electric start they are usually in a most awkward place to yank in a rope. They do, however have a couple of advantages over inboards.
1) The prop, etc. spends all of it's time when not spinning out of the water so no marine growth, especially in the tropics.
2) they can be had relatively cheaply, especially two strokes.
3) they work really well in reverse, especially if centered behind the rudder and with the tilt locked down. The prop wash past the rudder allows directional control without sternway, priceless.
4) If you can put an extension handle so that they can be steered from over the pushpit they are magic for tight manouvering.
5) Often they run from portable tanks so that the entire cumbustable thing becomes almost a non issue if the tanks are in a vented cockpit locker.
Just my two cents worth.