I'm a 4 stroke fan, my next boat may very well have one. However, for a heavy Parker sport cabin I would go with the 250 HPDI. (Actually, given the option I would go with the Evinrude 250, but I know you are limited to the Yamahas.)
The 250 HPDI has an all new 3342 cc block which compares favorably to the F225's 3352 cc block. Low end torque should be pretty much the same and the greater top-end of the HPDI will probably make it more efficient at 4000 RPM and above cruising speeds.
Check out some of the archives at
http://www.thehulltruth.com/ or
http://floridasportsman.zeroforum.com/zeroforum?id=16. Many guys over at those forums have recently gone through the same selection process.