I miss the low crowds, that's for sure. Even though I don't agree with franchising everything to death, I have to admit that everything they've done so far is an improvement over what was there before.
I must say that I do sort of miss the bubbly, watery Paradise Pier music, even though I like the new music better. Oh, and I miss the sun face on the Sun Wheel and the Mickey silhouette on California Screamin'. That's something I wish would have stayed the way it was.
ETA: Oh yeah, and I second the Strips Dips 'n Chips! I know it's silly especially since we have Toy Story Mania there now, but man I loved those strips and all the different sauces. I agree, they tasted SO much better than the stuff you get at Stage Door.