I've had connecting rooms at both Pop and Coronado. I didn't think there was any real differnece with regard to the connection of the rooms. It boils down to the amenities you want. With kids that old, I can't imagine you are going to be spending a whole lot of time in you room, so I'd suggest Pop. And, quite frankly, with kids that old you probably could get a "non-preferred" location and it wouldn't be that big of a deal - it would save you a couple hundred bucks, but the walk to your room would be 5 minutes longer. The downside to Pop is its location - so far away from MK. But, my kids are young so that's our favorite park. Wtih highschool kids, I question whether you will be spenindg more time at HS, Epcot and AK or even DTD. It may be a great location for you!
If I were in your situation, I'd do two connecting rooms at Pop without a preferred location. Between a Mod and a Value, you'll end up saving several hundred dollars and then the downgrade to the non preferred will save you a couple hundred bucks too.