I've stayed in both Epcot area resorts and MK area resorts. My preference - for many reasons - is the MK area resorts. Aside from MK being the park I'm at the most and my love for the Polynesian and Wilderness Lodge resorts, I also have to go with MK area resorts because that area strikes me as less busy and more secluded than the other places. Particularly is the feeling of seclusion prevalent at the Wilderness Lodge, which is still close to MK, but you still truly feel like you're way out in the woods somewhere. I'm also particularly fond of the view all-around Bay Lake and Seven Seas Lagoon from the boat dock at the Polynesian. Right around that time when evening is turning into night and the various resorts are lit up, and the sun is still going down........there's hardly a better view anywhere else in WDW. Then there's the TTC being so close by and the Epcot monorail. Sure, the MK area resorts do have bus transportation, but there's just something about being on that monorail that makes it more enjoyable. Sometimes on trips, I'll just get on the resort monorail even and ride it around the loop a time or two because I like being on it and I love being in WDW. I think the transportation options from the MK area resorts is much better than the simple bus options from the Epcot resorts (PLUS......the Epcot area resorts have the delay of the internal bus system to put up with, which you don't have at the MK area ones.)
I stayed at the Boardwalk Inn once (an Epcot area resort) and it just wasn't for me. To me, Epcot is one of those parks that's a middle-of-the-day stop while park-hopping or a pointed trip to meet my dining reservations. So the walkway to Epcot or DHS from the Boardwalk wasn't really all that terrific a perk. Then there's the boat ride to/from Epcot or DHS. I enjoy the boat rides in either area I'm staying in, but I think that the boat ride in the Epcot resorts area just takes so much longer than it should that by the time I reach my destination, I've checked my watch more than once. I will say, though, that the Boardwalk area is pretty cool-looking at night.
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Someone had previously mentioned the isolated feel the MK resorts have, but for me, that's an attribute. The Epcot area resorts have a cohesive vibe, so it makes sense to have them connected by walkways and boardwalk areas. But the MK resorts have these strong, stand alone identities. So,I really enjoy that they are isolated yet so easily accessed...with boats going in an out, the monorail, and the castle...it just screams Disney. i.e. iconic WDW at all corners.