Re: is there a major difference in performance between a 2 cyl. and a 4 cyl.?
The number of cylinders an engine has has no bearing on how much horsepower an engine can make. Horsepower per cylinder is what makes a multicylinder engines total horsepower. But one could design a 100 HP one cylinder engine just as easily as one could design and 100 HP 10 cylinder engine. Neither would be desireable because of the roughness (one cylinder) or the complexity (10 cylinder). So engine design is all about compromise. In the case of two cylinder Johnson/Evinrudes, they concentrated on two cylinder designs in the the smaller motors for decades and the reliability has been superb. Yes, there have been crossover years where two and three cylinder versions with the same HP existed but that's only because a mid range designs went to three cylinders. Higher HP versions went to V4, V6, and even V8 designs. Years ago Merc for example went with an inline six in their high HP versions which was a skinny motor but stuck up on the back of the boat like a tree stump.
Since your original question was about "the major differences" here they are. A two cylinder Johnny/Rude is a 747cc engine. A three cylinder Merc is 967cc. The J/E has a 2.42:1 gearcase and can swing 12 - 13 inch props. The Merc (non-big foot) has a 1.83:1 gearcase and swings a 10 inch prop. The Merc will be a tad faster once on plane. The J/E will get the same boat on plane quicker. How do I know this? Been there with both engines. Fuel consumption is a wash. 50 HP = 5 gallons per hour at wide open throttle give or take a tad and that ratio (10% of rated HP) is true for any marine engine.
For ease of service, simplicity, parts availability and overall reliability my choice is J/E. If high end performance and a little more smoothness is your only measure, go with the three cylinder Merc.