We have done a Merrytime cruise over Christmas, and last year we did a November cruise out of NYC last year that was both! 4 sea days,
Castaway Cay and WDW for ports. That said - I'd pick one or the other. The cruise seemed over-loaded with things to do - there didn't really seem time to relax that much.
Merrytime cruises have events pretty much throughout the cruise to celebrate the holiday. It's a much more spread out celebration, and easier to avoid pretty much all of it if you want to (other than the decorations, I suppose). Characters are about in their holiday garb, and Santa meets children in the atrium (though the line for that can be looooong!). There are craft events, and holiday cookies and hot cocoa in the atrium, and buttered rum available for purchase in the evenings.
MDAS cruises have a single day dedicated to Marvel. You can't avoid Marvel. It's everywhere. There are 2 (free) ticketed meet and greets - which do "sell" out. There are marvel characters and Disney characters in Marvel garb in set meet-and-greet areas (often with long lines) and a handful of walk-around characters that do ad-hoc photos and autographs - but you may have to follow them around for a bit. There's a special Dr. Strange stage show. And the evening deck show is
the best deck show I've seen on a Disney ship. There were sessions to draw marvel characters, and you could check out iPads to read digital comics, and they had trivia sessions and a costume event - honestly, we didn't get to do everything, and it was a full, exhausting, fun day! The best part was the costumes on the guests. We saw everything from themed shirts to cosplay, and all of it very fun to watch!
Putting both of these together is exhausting. Personally, I'd do MDAS again in a heartbeat (or SWDAS). The Merrytime cruise is fun (this was the second we've done, the first actually over Christmas) and the photos and decor was beautiful, but I think the other themed cruises give you one crazy day, then the rest to enjoy your normal vacation.