Resale value is the worst reason for picking a bike. Bikes all have crappy resale value. Instead, buy what turns you on. If you buy it, you're gonna have to like it. Have you ridden either? Treks and Cannondales can be found in virtually every town. If you have to travel an hour or two to do a test ride, it's generally worth it. Buy the one that fits and feels the best.
In terms of the bikes themselves, it's kind of toss up. Trek's new CF frames show that Trek really has its game goin' on; however I'm not sure if those frame ideals work in aluminum or not. I've always thought they were a bit long in the top tube, but that might be just my own bias. The component spec on the 2.3 is certainly good. Cannondale are experts at making aluminum bikes that perform well, and the CAAD series is legendary. The CAAD9 lives up to the reputation. It used to be that Cannondale's, with the huge frame tubes they had at the time, road like a grocery cart over railroad tracks. Now that's completely different. I've a good friend in New Zealand who has been riding a CAAD9 for some time. He tends to make long rides, often spending a lot of time on "metal" roads (don't ask why NZeders call gravel roads "metal" roads) and other less than smooth surfaces. He has zero complaints about the ride. I think the CAAD9 is the better looking bike. While it has a mostly traditional geometry, it looks new and aggressive. The component spec on the 'dale is better than that of the Trek. The 'dale uses a mixture of SRAM Rival and Force, both of which shift a bit better and are a bit more robust than Shimano 105 (the gruppo on the Trek). If I were to consider buying a new frame, Cannondale would be at the top of my list (For reference, I've a Look 595, now.)
Both companies offer excellent--more than excellent--customer service, so there are no worries there.
It all comes down to how you think they ride/feel, and/or how much each of them tickles your gouch.