The big negative at Contemporary (for some people anyway), you already mentioned, the lack of a theme that screams Disney in a world where many luxury hotel chains now look quite a bit like the Contemporary does. There are little Disney touches throughout the resort, but not an immersive theme the same way Poly or WIlderness Lodge or certain other resort are.
The big negative at Boardwalk, IMHO, is a lack of a food court with ample seating. Because the big draw of the Boardwalk resort is the Boardwalk itself, there are plenty of places to grab a bite. The line for the Bakery gets crazy especially in the morning. But if you don't want to eat outside, maybe it's a hot and humid or cold and rainy or otherwise miserable day, then it's a question of finding a place to eat inside or back in your room (which might not be convenient). Whereas Contempo Cafe, in the experiences I've had there, has decent enough seating, good selection, and efficient at making food & moving you along. Plus there's also The Wave, which is not a counter service or food court, it's a table service restaurant, and it also doesn't scream Disney whimsy either, but the food is great, and it's practically never busy. And if you wind up with a room at the Contemporary in the main building as opposed to a tower room, it's also likely easier to bring food back to the room. I'm certainly not trying to sound like a foodie (though the fact that I'm trying to drop another 25 pounds before my next trip so I can gorge guilt-free probably makes me think about food too much!). But the way I see it, the amount of time you can save by getting a quick counter service meal when that's what you want is time you can spend having more fun.
Other than that, like most other folks, I'd think about the park(s) where you think you'd spend more time - the Contemporary is a transfer/two monorail ride to Epcot, and the Boardwalk is a single bus ride (with potential extra stops to other resorts, or crowded buses because they went to other resorts first) to MK. But for some people, the monorail IS a ride, an experience to be enjoyed, and IMHO bus rides always feel like somewhat-necessary evils and not unique experiences to be savored. If you wanted to ride a monorail from Boardwalk to MK, you'd have to walk through International Gateway and through Future World to the main entrance first, not the best use of time.
And here's something I hate bringing up, because my best friend is a professional and hilarious circus clown and it's irksome the way some people have knee-jerk reactions to clowns, but...does you DD like clowns? Ironically, because of my situation, my wife is NOT a fan of clowns, and while she enjoyed riding the Keister Coaster slide well enough, looking at the clown face on the front side of it was not her idea of a good time. Plus we come from the Jersey shore area, so that style of resort is not all that unique to us, even if we don't stay in that style of resort very much because we live so close.
If none of that helps, consider this - have you thought about a split stay, half in one resort, half in the other? If you don't know, Disney's Bell Services will even move your bags for you, make it easy-peasy (wouldn't it be great if they'd pack for you, too? THAT would save some serious time!).
