To those of you who say Pop's transportation is the best you've experienced, I'd be curious to know where else you've stayed.
We chose to stay at Pop several times, because transportation was not our main concern; our budget was. Then after a few long waits leaving the parks at night (not during peak season, either) we switched priorities a bit.
I know that everyone has a different experience on their trips, but this happened to us more than once. We are patient people, but we've seen the queue at MK overflowing on more than one occasion. Even when they send several buses for Pop, there was a significant wait, often ending with standing on the ride back.
I think the major difference is that you will often see less people waiting in line for the deluxe buses than you will for the values. So while they may be sending the same amount of buses (maybe even more for the values) for all the resorts, the value ones will fill up faster at the end of the night. I've just never seen a queue for any of the deluxes be overrun with people at a park, at the end of the night. If there's a shorter line at a moderate and I can get a seat, I don't mind if it stops at the other resorts first. To me, it's better than standing in line or on a bus, after standing/walking all day, no matter how comfortable my mickey Crocs are!
In short, if transportation is a top priority, I would suggest considering a moderate or deluxe resort, if your budget allows.