Oh, thought about one more detail worth considering -- especially if you're looking at the Whaler -- weather. Specifically rain and/or cold.
The center console/open bow boats are absoultely amazing on nice days, there's no question. But on a rainy/cold day, the closed bow + canvas on a cuddy is a big advantage when you're moving around, or even just trolling.
Ditto what Summerun said about motors -- IMHO a Yamaha or Honda 4-stroke is what you want. For both the main and kicker. This gets you out of mix-in oil, better fuel economy and a completely unified fuel system (e.g. a single big tank).
The points here about compromise are of course correct -- good luck in your search!
Maybe this should be asked in a different thread? But, what is wrong with a merc 4-stroke? They have been building longer than the other two you mentioned combined. I'm sure they are as efficient as the others. I have not heard any bad reports on them. To be honest I have never really heard any reports on them. When I bought my boat< i looked into a Verado, I couldnt come anywhere near the price of the yamaha 150. I could have bought a 150 optimax for 1500 less but wanted to stay away from 2-strokes. I am totally happy with what I have, I think I would have been as happy with a merc though. As far as kickers go, I couldnt imagine anything other than a t-8.