Hi Dazza
We are just back from 3 weeks with a similar group to yours...myself and DH (both 30 somethings), DD 4 and DS 2 and a bit, plus my 60 something Mother.
This was DH and my 9th trip, but our 4th trip with the kids and Mum. We are planning to all go again in Oct, so its not all bad, honest! Bonus of taking a relative is you get to go out on the odd night without the kids

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OK, first, my biggest and most important tip...DONT TRY TO DO TOO MUCH! Many first time visitors dont have any idea just how big and spread out the attractions are. We have just got back and only managed 4 Disney parks and Sea World! To be really, really honest with you, with kids of your ages, then Universal / IOA is not going to be that great for them. Others disagree, but although we loved these parks when visited as a couple, with two under 5s they became large and tiring. There are only a few rides that your 4 year old can do and even less that your 2 year old will get on. We have skipped these on recent trips.If you do decide on the Flex Ticket, then I wouldnt allocate more than one day at each here. Sea World is fantastic for under 5s and 2 days is easily needed.
Again, personally, I would miss Busch Gardens this trip. If you are planning on coming again when your boys are bigger, then leave it out.
Kennedy Space Center is EXCELLENT and a great day - you will love this.
Its worth taking a trip over the to the Gulf Coast as well (I would skip Busch Gardens and do this). You can get on the Sea Screamer at Clearwater (very fast speedboat to see the dolphins), and your kids will LOVE the beach.
Our 2 year olds fave thing was the characters at Disney, so I would highly recommend you book a character meal. He also enjoyed the parades, Playhouse Disney, Voyage of the little Mermaid, Beauty & the Beast show at MGM, all the shows, the dancing fountains, Living Seas, The Land, El Rio De Tempo and character bus all at Epcot, Kilimanjaro Safaris, Triceratops Spin, Flights Of Wonder, Lion King Show, Pocahontas Forest friends and the adventure playground at Animal Kingdom. He enjoyed almost everything at Magic Kingdom! You wont be stuck for things for him to do!
Another tip is be flexible! It will be VERY VERY VERY hot when you go. There is no point dragging hot, tired, grumpy kids round a theme park. My advice is get there early when its cooler and less crowded. LEAVE when you stop having fun, even if its only 11am. You can always come back later in the day. For this reason, I always choose a flexible ticket for Disney. Unfortunately, the Disney Tickets are changing, so Im not sure whats going to be on offer, but I would advice something like the old 10 day ticket which included all the main parks plus water parks. The days dont run consecutively, so you have good flexibility.
We do find that elderly relatives do tend to get grumpy if kept in a Theme Park environment for too long. To calm the murky waters of MILs that get tetchy, may I recommend a trip to Celebration, frequent excursions to the Wal-Mart and if she is REALLY becoming a pain, Dive With The Sharks at Sea World...thats not the planned Dive, you just chuck them in when you pass the tank

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Have fun!
Allie