When I bought my single (6.2L) 2900 in November of 2006 I had a chance to get a twin for about $5K less... but it was clear the heck in Florida (I live in WA State). The broker from whom I bought mine (in Lake of the Ozarks, MO) convinced me that the the saltwater and Florida sun had done more damage on the twin-version than the one I eventually bought in Missouri. Mine spent most of it's time on a large boatlift in it's slip and when it hit water it was FRESH water. She had 57 hours in five years---I put 57 hours on it in the first four MONTHS!
Advantages to the single engine are more room in the engine compartment to do things, store stuff... less maintenance obviously and typically less expensive overall. But it's way less manueverable---although I remember the yacht broker telling me the space between the two V-6 outdrives on the twin 2900 weren't far enough apart to TRULY take advantage of a twin engine's characteristics (turning in it's own space, walking it sideways to a dock, etc...) Probably just a sales pitch, but as far as performance goes... I can do 40MPH and get on plane in a decent time. Although if there's more than six adults in the rear salon I can't get on plane unless two or more of them step down into the cabin... especially if I'm pulling my JetSki and want to get on plane! I added one of those StingRay wings on the outdrive which I think made a difference, too. Getting on plane will probably be a rare thing though, when gas is $5/gallon on the water!
I tease my boating friends with their twin engines that they're big pussies and aren't as good as a driver as me doing what I do with a single engine. Bottom line is if you can drive a boat as big as a 2900 SCR with a single engine I think you're doing a pretty decent job!