For us, it's a matter of comparing an on-site HOTEL ROOM versus an off-site VACATION HOME. There is a big difference for our family. We have 2 kids and all of us get better sleep when we don't have to share a tiny room. We usually rent a home or condo (both have been 3 bedroom, 3 bathroom, full kitchen, pool, and laundry facility) fully decorated in Disney gear, I might add, for as little as $79 per night (off season, in October). We can afford to go every year (for the last 3 years and probably this year too) because we stay in a off-site home (NOT a typical hotel rooom. If this were the case, then I'd spend the extra cash to stay on-site.)
It depends on your priorities for your vacation. From the front door of our most recent vacation condo to the gates of Magic Kingdom took us less than 20 minutes (that included parking, taking the tram, the monorail and getting through the gates). Is that typical with all other Disney transportation? I don't know, I've never stayed on site, but that seems pretty quick to me. I personally would rather sit in the comfort of my own car after a long, warm day at the parks than on a loud, warm bus, but that's just me. (Perhaps I don't see much benefit to Disney transportation because we go during the off season and spend VERY little time getting to our van and leaving the parks. It's always been very quick, very convenient and we've never encountered any traffic while coming to or from the parks.)
Our priorities are to have personal space for sleeping (kids in one room, my husband and I in another), breakfast in our home (we get better food, quicker and cheaper) and an opportunity to return next year because we haven't spent too much on a room that we won't spend oodles of time in. The house it quieter - I don't have to listen to someone yelling at their kids in the room next door, kids running down the hallway as I'm falling asleep, etc. We just prefer the convenience, quiet and lower cost of a vacation home rental to the Disney hotel resorts.
Because we go in the off season, EMH wouldn't be a necessary benefit for us. We usually make it through the entire park we're in on any given day, so we don't need the extra time to go on the attractions while the "day guests" are not in the park.
It all depends on what makes you happy. Good luck with your decision.