I really think the difference is more with the resort itself. I'm pretty sure there is a little bit of extra square footage with the mods but honestly, I didn't see a big difference in room size from the mods to the values. We stayed at POR in Nov - I really liked the fridge in the room (for no extra charge per day), especially for a longer stay. Nice to be able to bring leftovers from the restuarants and store drinks without having to run back and forth to the food courts. There was a curtain between the sink and bed area which was nice. And then your standard beds and table and two chairs. I think that yes, if you're in the room for a long period of time, you do kind of feel "on top of eachother" at both places. For us it wasn't too bad - one boy would play handheld video games, one might watch tv.
What I really liked about the mods though was the overall resort. The theming is more specific to the resort type as opposed to all Disney theming like you have at the values. When you did feel cramped, you could take a walk (lots of walkways, or to the food court, wherever) - and it was just so scenic. Walking along the river at POR or sitting on a bench. At CSR, there were so many quiet spaces with fountains and the buildings surrounding the lake and being all lit up at night was just beautiful. It was just really, really nice. We rented bikes one day. We could find quiet nooks at the pools. There was just a really peaceful and relaxing vibe at the mods. You were still at Disney but it was almost like being on two separate vacations because you had all the best of Disney and then all the relaxation and theming of your resort.
I don't mean to in any way diminish the values either because we like those resorts too. I just felt much more peaceful at the mods. We did do a trip one year with two rooms at a value becuase my dad came so there were five of us and the extra space was really nice. Definately a little more privacy.
It really comes down to how much you think you'll be in the room. I just know for me, I loved being outdoors and soaking up the atmosphere of the mods. Sorry for rambling - I'm remembering what a nice trip it was. I wish I was there now.....

I hope you have a great vacation where ever you decide to stay.