I've got a very similar trip booked for next month and have previously visited in 2011, so hopefully I'll be able to help.
Flying with Virgin is the best option - I flew with Monarch (I'm not sure they fly to Orlando any more anyway) in 2011 and I can say for sure that Virgin is the way.
September is the best time to go - whilst Disney will be packed whenever you go, the other parks should be quiet and you'll have no problem fitting everything into two weeks.
Whilst I've never been in a Disney hotel, I personally would recommend a villa on a road just off I-Drive. To my knowledge, it costs no more than three rooms at a Disney hotel and you get extra freedom and (almost always) a private pool. The one we're staying in is only 10 minutes from Disney, 15 minutes from Universal and 20 minutes from SeaWorld, but you can get closer (the price goes up the closer you get). We'll be hiring a car from the airport, it's more convenient than public transport, if more expensive.
Dining - my favourite restaurants in 2011 were Denny's (somewhere near our villa) and Hard Rock Café (inside Universal).
Parks - Disney, Universal, SeaWorld and Busch Gardens are not optional. Discovery Cove, whilst expensive, turned out to be on of the best days of the entire trip, so fitting that it would be great. And if you have some time, the waterparks (Disney's Typhoon Lagoon, Disney's Blizzard Beach, Wet 'n' Wild, and Aquatica) are fantastic.
My trip for this year works out at £2500PP. Don't know if this works for you, but there's plenty of areas that could be trimmed to make it cheaper.
Enjoy your holiday!
Burniel | Great at theme park knowledge, not so great at designing signatures.