Probably because of money, but sometimes I wonder if that even makes sense (no pun intended). They want you to upgrade to the latest model, like the Evo 3D at the time we should've received Sense 2. The problem with that logic is that most people don't know what version of Sense they have and they don't care. Few regular users bother to change their homescreens from the factory settings. Some don't know how, others only use the app drawer. The people most likely to know about different versions of Sense and which phone have which version are people that root their phones, and they're able to flash custom roms with whichever version of Sense they want. Yes, some of them will upgrade to a phone that has it native, but the number of people that know this is probably small compared to the number of people with the phone. Most people wait for their upgrade. Unless someone is already in the store and a Sprint employee tells them that this particular phone they're selling has an upgraded version of what they have, but if they're already in the store they probably are already looking to upgrade.
Maybe this logic is flawed, but I don't see how keeping Sense 1.0 on the Evo could drive up sales that much. Maybe it would a little, but enough to really matter?
I don't think it has anything to do with the specs either. So I'm not sure what it is. It could still be the money, corporations seem to care about a few hundred bucks even when they're making billions.