We were recently faced with a similar dilemma. We called the manufacturer (Edgewater)and talked with a member of their technical staff about what would best power the boat we were purchasing. They gave us a two-stroke and four-stroke option and all the reasons behind each.
We also visited J.D.Power and Associates at:
http://www.jdpower.com/cc/boats/index.jsp Once you click on this link (or cut and paste), click on "engine quality and performance" on the left hand side of your screen. It is a pop-up screen, so be sure not to block pop-ups.
You'll be able to read their take on outboards.
"J.D. Power and Associates Reports: Technology Plays Major Role in Marine Engine Purchase Decisions by Consumers. Evinrude and Yamaha Rank Highest in Customer Satisfaction Among Outboard Engines."
We feel that this research allowed us to make a very informed decision.
We currently have a Yamaha on our Grady White and have added a Yamaha to our Edgewater. We couldn't be happier with them. (now, don't boo but we did go with a two stroke on the small Edgewater because of the weight issue) Because of technological advancements, the two-strokes being manufactured today are nothing like the old smokers of the past.