My family is originally from Southern California, and we have personal connections to Disneyland. Both of my grandfathers worked on the park. My maternal grandfather was a steamfitter who laid pipe. My paternal grandfather was a carpenter who worked on Main Street and at least one ride that I know of (the original Flight to the Moon). So my connection to Disney parks goes way back before my birth and starts with Disneyland not WDW.
Having said that, however, and despite the fact that Disneyland has more attractions (and, as you said, the best attraction at any park with Indy), I still prefer the experience of the Magic Kingdom. The smallness of Disneyland is significant, especially when you've been to MK. The smallness stands out. I mean, man alive, have you ever been on Main Street at Disneyland at closing time? You think MK Main Street gets crowded! Also, the clutter of Anaheim being all around the park has always driven me crazy. Now, this has gotten better since they turned Disneyland into a resort, because there is somewhat of a buffer right outside of the park with Downtown Disney and DCA. But, DCA is so dang close, there is scarcely any breathing room between the parks. Also, supposedly, the castle was made larger at MK by Roy's insistence because Walt had lamented that he wished he'd made the castle at Disneyland bigger. The thing is, Walt wanted more room when he built Disneyland, he just ran out of money. So MK fulfills that wish.
For the record, from what I read about Walt, if he were still alive, he would have become totally bored of Disneyland by the early 1970s and moved on to other things. In fact, he was already moving on to Epcot in his thinking and pulling away from Disneyland by 1966. If he were somehow still in good health in 2010, he would probably be trying to build a moon base or something by now.