I touched on the comparison in a blog post entitled Compare and Contrast a few weeks ago, but thought it might make some sense to elaborate on the differences. Magic Kingdom is much bigger.
Other than that, Disneyland beats Florida's flagship park hands down, I believe. Oh, Florida has things to recommend it. The Carousel of Progress is really fun. I don't know why really, but both of my kids love it. And I appreciate it and what it represents for Disney, and I value the connection to Walt himself. We also really enjoy the Tomorrowland Transit Authority, with its slow paced tour of Tomorrowland.
I have to give the edge to California, however, on Fantasylands. I am amazed that they fit as much as they do into such a small space. Storybookland, Alice in Wonderland, Mr Toad, the Casey train ride, and Pinocchio's Daring Journey are all only found in Disneyland. Florida does have Winnie the Pooh, (which is in the California park but not in Fantasyland, and which I've not ridden there) and Mickey's Philharmagic (a major plus for Florida), but otherwise, there isn't much comparison - Disneyland wins the battle.
I don't much care where things are placed. I have read "complaints" (mild, but still offered as negative criticism) that the placement of Splash Mountain and Big Thunder Mountain Railroad so close together in Frontierland at the MK is not ideal, but to me, who experienced the Magic Kingdom much more than, and prior to, Disneyland, the separate nature of the rides in California feels odd. I will say, however, that the Monsters Inc. Laugh Floor seems really out of place in Tomorrowland, and that I don't like the Stitch attraction at all, but that's got more to do with theming than with location.
Pirates of the Caribbean is, hands down, better in California than in Florida. The Castle is better in Florida, so much more imposing. It's the first one I saw, so it remains the gold standard for me. The train ride around the park is better in California, if only because of those dioramas between Tomorrowland and the Main Street Station. There's no Matterhorn in Florida, so even though I think the rollercoaster itself doesn't hold a candle to something like, oh, say, Expedition Everest, we're not including Animal Kingdom for the sake of this comparison. Advantage California again.
The ride on Space Mountain in California is better, though that may change after this refurbishment that is going on in Florida. Disneyland has Indiana Jones with its theming and exciting ride, Florida has nothing really like it in the Magic Kingdom. Florida has the Country Bear Jamboree, which is fun, but, well, sort of old. California has the Nemo Subs, which might not be as good as the old 20K Leagues, but is still better than the nothing offered in its place in Florida. And the Aladdin Flying Carpets are nothing to get too excited about in Florida. A time filler that loads and unloads quicker than Dumbo (which both parks have).
Florida has Tony's, the Crystal Palace, the Princess thing in the Castle, and a handful of good counter service options for dining. California has the Blue Bayou, which has a very cool atmosphere, and a couple other table service offerings. I like the food choices at Tony's better, but have to admit that there isn't a huge advantage to the Magic Kingdom. In fact, I think Disneyland might have more offerings for table service, but I'm not sure. When in California we've generally eaten outside the parks.
Toontown in California is much, much better than its counterpart in Florida. Enough said.
The smaller size makes Disneyland feel very crowded, whether it is or isn't. (I think that both times I've been there, it actually WAS quite crowded.) This isn't as big of a negative as one might otherwise think.
Advantage overall: Disneyland. In fact, I don't think it's even close.