We will only fly into SNA, I find the convenience of how close it is to the parks far outweighs the extra cost. We also take a taxi from the airport to the hotel to any extra cost for the flights is made up in the savings on transportation, at least that's what I tell myself! We also catch a ferry to Seattle and stay overnight so we can catch the first flight of the day. It gets us into SNA around 10:30am so we are in the parks by noon!
As for hotels, we stayed at the DLH for the first trip we took with DS but after that we have stayed at various motels along Harbour Blvd. You really cannot beat how close they are, especially since we like to take a mid day break.
We have stayed at 3 different motels along Harbour, each had their pros and cons.
Park Vue Inn: we stayed there March 2012. They have a hot breakfast and at the time we stayed they also had free bottles of water, fruit and cookies in the lobby as well as an evening "dinner" hour with one hot dish served between 6-7 pm. They have since stopped everything except the hot breakfast.
Desert Inn & Suites: we have stayed there twice, April 2013 and March 2014. Great price if you book far enough in advance. They also have fantastic suite configurations for up to 10 people. They have a small breakfast with pastries, toast, hard boiled eggs, coffee, tea, juice and cereal.
Castle Inn: we stayed there September 2013 when we decided to go at the last minute. Out of the three places, this one was the furthest but still within 10 minutes walk even with our 8 year old's slow walking pace! No breakfast.
We are heading back in less than a month and we had a reservation at DI&S but since my SIL is joining us, I changed the reservation to one at PVI. The per day cost is $20 more but I figured that over the course of the 5 days we will save at least that much by being able to have breakfast there.
I've booked everything myself after the first trip and I find that I can get a much better deal by booking separately.