An excellent point for discussion. The answer I think will depend on how you like to cruise.
We have a 32' flybridge with a covered aft cockpit, which we love. At anchor or at the dock we can have the doors open to the cockpit all the time, come rain or shine, during the cruising season along the BC coast. The forward stateroom doesn't get too rambunctious when the waves or wind pipe up we find.
However, we determined that we needed a second stateroom and so have been on a quest for the last few months for the next boat, looking in the 40' range. Initially we were looking for the same arrangement as we currently have, but with the second stateroom.
What we discovered is that generally speaking, the forward stateroom/aft covered cockpit vessels suffered from a lack of personal storage space in the staterooms. Yes, we looked closely at a Mainship 400 but were discouraged by its lack of locker storage, particularly in the master stateroom.
Once we started looking at aft cabin models, we discovered that they had much more storage space in the master staterooms, albeit at the expense of losing the covered aft cockpit. You also gain a second head usually, and significant separation from any guests you might have on board.
For example, the Monk 36 has a much more usable master stateroom than the Mainship 400.
But all of that comes down to how you use the boat. For relatively short cruises, I don't think personal storage is a big deal, but if you going to be away from laundry services, for example, or like to dress appropriately for every occasion (I have no idea how that works myself.) you might want the storage.
If you like to sit in your cockpit at anchor during a rainstorm and watch the bears flip rocks on shore, then the forward cabin version might be the better choice.
There are also the covered sundeck models, which are kind of a blend of the two types mentioned above, but which I know little about.
