Hi! Well, I can answer some of your questions...
For the plane ride, it totally depends on the kid. One of mine did great on a long plane ride, but he's mr easygoing all the time. My other son, not so much. Be prepared with snacks and entertainment. A portable DVD player would probably be a good investment if you don't already have one.
Second, for the hotel choices, I would personally pick the
Disneyland hotel, but honestly I've never stayed in either. We did stay at the Grand Californian, and it was really nice, but not worth shelling out the big bucks, IMHO. Disneyland hotel has wonderful, classic Disney theming. Paradise Pier does not have the same level of theming, but it does have an entrance to California Adventure. This being said, it is just about as far to walk from any of the resort hotels to Disneyland as it is to stay across Harbor Blvd at one of the Good Neighbor hotels, and you get most if not all the benefits of being a resort guest (i.e. extra magic hours). And the walk between Disneyland and Calif Advent. is only a couple hundred yards at most. We've stayed at the HoJo (nice, but a little too far away for walking w/ little ones) and the Tropicana (Nice enough, and you can't get much closer to the crosswalk to the park entrance. Either would be about half the price of the Disney hotels.
Finally, the food!!!! I've not done the dining plan. We have always driven and had a fridge in the hotel room, so we stocked up on snacks & drinks. There are many, many restaurants within walking distance of the Harbor Blvd hotels, Millie's restaurant was wonderful! and there is a Denny's for a decent filling breakfast if that's your thing. If you stay onsite, you have less access to these restaurants, and less inclination to spend your money outside Disney property (hmm, almost like they planned it that way...). For onsite faire, Storyteller's Cafe in the Grand Californian has a character breakfast (buffet) with Chip and Dale being the main characters, which we enjoyed, but the kids liked nothing on the buffet, which was a major waste of a lot of money. Elsewhere in the parks, you can get a Dole Whip on the path to Adventureland, and I can't think of anywhere I'd rather try than the Blue Bayou which overlooks the Pirates of the Caribbean beginning part of the ride, so the atmosphere is dark and peaceful.
Hope some of this helps, and I'm glad to answer any other questions you have!