If you are going with a seperate system (i.e. seperate tweet and passive crossover), I'd stay with the 6.5" size.
If you go with multi elements (that have the tweet and super tweet within the speaker assembly), I'd bypass the 6.5's and go with 6X9's. The reason is the 6x9 has more cone area (i.e. louder), generally will have more power handling capability (over 6.5's), and more mid bass.
The advantages of a seperate system is the woofer cone is one piece instead of having a center pole protruding through the cone for the tweet assembly. You can make an arguement that a seperate tweet is also better in a car for imaging but I don't think that applies so much in a boat (open air environment).
To me the best thing to look for is what product will give you the best sound quality with the most SPL at the same time in a boat.