If the motor is set up correctly and propped correctly, there isn't a lot of difference. Other than fuel consumption, smoke (or lack of), etc. Weight is an issue on boats that are too small for the motor, like a lot of guys putting 25's on 1232's and 1432's. Or overpowering a bass boat rated for 150 hp, with a 225 or 250. Then weight becomes a problem. BIG problem with tiller steer motors that have manual tilt, unless it's got the tilt assist which is sweet.
There's always going to be the die hard smokers, and I were one of those until I personally bought one. Now I won't go back to a smoker. I thought I was going to hate it and bought it to just re-sell the whole rig. Ended up keeping the motor and selling the boat. I've had the motor for about 4 years now. Put about 50 hours or thereabouts on it. I've not had to make one single repair to it yet. Other than having to clean the carb once, it sat almost 4 months (my own fault). It was used, with unknown hours on it when I bought it. I had to force myself to think outside the box.
Ran a 2 stroke 25 (25MSHU)--twin cylinder twin carb yamaha on my boat for a while. Then sold it and put my 25 4 stroke on it. The MPH is almost exactly the same. The 4 stroke is on plane faster.