September has traditionally been quiet, but is becoming much busier now with a few events happening that month. The start of Halloween time always brings lots of people, and there's an event called Dapper Day which has quite a large following too. We were there for the middle weekend of September last year and it was hot and crowded, even more so than the Labor Day long weekend! It was better than being at home lol! But it did take some getting used to!
I would recommend late February/early March. On our first trip we were there the last week of February and it was so nice and quiet. A lot of rides were walk ons and it was so easy to get around without having to thread our way through large crowds. The shows were easy to get good spots for too. The days were nice - jeans and t-shirt kind of weather - but the nights were quite chilly. This year we were there for one day on 4th March and again, it was super quiet and perfect weather too! The spring version of Dapper Day seems to happen in early March. If your visit coincides with it, that weekend will be pretty busy, but it does tend to be mostly locals that go, so it shouldn't affect your week days too much. They do offer spectacularly discounted rates at the Disney owned hotels, so it might be worth attending (you just dress up nice for your day in the parks) and make your trip REALLY special by spending a few nights at the Disneyland Hotel.
If you go in the off season, you will need to be prepared for ride/show closures, as that is when they tend to do most of their maintenance. However, next year will probably be quite good for closures since they've done so much this year in the lead up to the 60th anniversary. If you go in March next year (not sure whether that's too soon for you), you will catch the tail end of the celebration. September might be too late. Also be aware that in the off season, most of the shows are only shown on weekends (just off the top of my head, the fireworks, Fantasmic! and Mickey and the Magical Map). It's easy to work around. Just make sure you include a couple of weekend days/nights to catch all the shows you want. World of Colour has traditionally been on every night, and the Aladdin show is on daily too.
Personally I would not consider a
Disney cruise an affordable way to travel. Also, there are not nearly as many Disney cruises that leave from the LA area. There may be other cruise lines that offer good specials from LA (I think there are a few that leave from Long Beach), but obviously they will not be as magical as the Disney ones. I'm not a cruiser, but there are heaps of people here who have done Disney and other cruises who can chime in.
Personally an included breakfast is not a high priority for me. A lot of the included breakfasts are very basic (just cereal, toast and pastries). We just bought some cereal, milk, juice and yoghurt from the 7-11 (5 minute walk) and made our own breakfasts when it wasn't included. When it was included, we tended to just grab a quick bagel to tide us over, then have a late brunch in the parks or DTD anyway.
I meant to say in my first post too (but I'm sure you're already aware), definitely make sure you get good, fully comprehensive travel insurance. You definitely don't want to be out of pocket for medical expenses over there! With your daughter's pre-existing condition, I would look at travel insurance first (even though it's not as exciting lol!) just so you're ready to purchase a policy as soon as you start making bookings. A lot of travel insurance companies will cover pre-existing conditions for an additional fee.