Pros and cons
Four–strokes have a long list of positives. They run more quietly and smoothly than two–stroke engines, particularly at idle speeds, making them the ideal choice for trolling. They are more fuel efficient–generally by at least a third, even more at idle speeds. They offer an extended range and produce almost no smoke. They are also extremely reliable. What all of this means is that operating costs are lower than for two–strokes and downtime and environmental impact are minimized. Additionally, unlike their two–stroke brothers, they can be used on any body of water.
That's not to say the four–strokes don't have their share of negatives. The more complicated construction means your initial outlay is higher, though much of the difference can be recouped over time because fuel costs are lower. Four–strokes are heavier, they're hard to transport, there are more parts to malfunction and repairs tend to be costlier. Other considerations are that crankcase oil and filters must be changed on a regular basis, there are not as many mechanics trained and certified in four–stroke repair, and–a potential deal–breaker–the largest available four–stroke is about 130 horsepower. If you need more than that, you'll have to opt for dual engines (if your boat can accommodate them), and shell out double the cash.
Two–strokes have their own merits. Simpler construction has the sparkplug firing once every revolution, vice twice, and eliminating valves, which in turn lowers both weight (particularly significant in smaller boats) and cost. It also adds power (speed and acceleration) and is easier to repair–a rather significant list of pluses. There are fewer things that can go wrong with the two–stroke, but when something does malfunction, there's a ready supply of parts and knowledgeable mechanics to fix the problem. You won't have to change the crankcase oil and filter as often, either. Finally, the newer–two stroke engines are getting cleaner and more fuel efficient, and some now come with direct fuel injection, eliminating the need to premix oil and gas.
Nevertheless, two–strokes are noisier, smokier and less fuel efficient–all significant environmental issues–and idling is rougher. If you purchase a no–oil injection model, you still have to mix gas and oil yourself. Operating costs are higher, effective range is reduced, the motor can be harder to start, spark plug fouling can be a problem and the carburetors have a tendency to gum up if they're not used frequently enough.
Clearly there are many considerations when making your choice. For now, price could well be the ultimate determinant. In the future, however, as prices for the four–stroke continue to drop and a wider range of horsepower becomes available, the two–stroke may become a less attractive alternative.