We have traveled out to Disneyland several times and stayed at a few different places. We typically fly into either John Wayne (SNA) or Long Beach. Our last trip we used SNA. It's a Southwest Hub. I've used Super Shuttle for transportation and been pleased with the service at SNA. Many trips we rent a car because we explore a bit more.
I'll admit I'm a hotel snob. I typically travel with my children so I look for a good pool, location and safety. I hate hotels that open to the outside, so I typically avoid those. (Especially if it is just me and kids.)
There is a Holiday Inn on Manchester. It was very nice when we stayed there last, but you can't walk to the parks from it. It had a nice pool and free parking. Some negatives Location and lack of dining.
The Park Sheraton on Harbour is still my favorite. It is one of the few hotels in the area with a balcony and you can get a theme park view which offers a good view of fireworks. (IMO it was better than what we had staying in a Disney Resort but you don't get the soundtrack.) It's within walking distance but a little further down Harbour. We didn't find the walk bad compared to what you experience with everything in Florida. This is as far down as I would recommend if you plan to walk to the parks.
Last trip we stayed at the Sheraton Garden Grove. This was a very pleasant surprise. It's pretty much as far down on Harbour as you can get before you leave the Disney Resort Area. We happened to be there during August one of the busiest weekends, so hotel choices felt limited. (I wanted to try the Red Lion, which I've heard good things about.) I don't recommend thinking to walk from this area. It's a good distance. They had a shuttle to and from the park that was very affordable. ($2.00/day, I think. My DD was free.) It was never crowded and we got there for Rope Drop and stayed late. It was combined with 3 other hotels in the same area. There is a Target pretty much right across the street. The negatives were parking (charge per day) and lack of dining options. But I'd still stay here again.
Most of the hotels in the area meet a fairly high standard based on my readings. I have friends that stayed in the Hampton directly across from Main Gate and they were pleased. (I've heard parking is a challenge in this area.)
I can't rave enough about the Disneyland Hotel. By far our favorite Disney Resort. Tops anything we have tried in Florida. We don't stay here often but dream of being able to go back.