If you have to travel in April...ugh, the crowds...then WDW should be fine. Space Mountain is closing for an extended refurb on April 19th, so if you are traveling before then at least you can catch one last ride before they make the coaster safe again (just kidding!). Otherwise all your favorites will still be in place, with the exception of the Hall of Presidents which won't open until July. Also, keep in mind that the Yeti in Expedition Everest is currently motion-less until that coaster is rehabbed (no dates set as yet). As for places to stay at WDW, I still think the resorts are having some great deals...check Mousesavers.com. Also, many of the non-Disney hotels in the area are offering great deals, so you might want to do a little more digging.
Another option might be to go to Tampa and visit Busch Gardens Africa. They also have a water park there, and the Lowry Park Zoo is nearby. If you have not been to BGA before, it should be a great option for a shorter stay. If you are interested in BGA, there are other folk on this site that know a lot more about it than I do, so just let us know what you are thinking and we'll go from there!
Most of the rides have height restrictions of 48" or less with only three rides having restrictions higher. Those rides are the Dueling Dragons, the Hulk Coaster and Doctor Doom's Fearfall. You can find out the height restrictions on their site for all the rides that have one.
There is plenty of things to do including shows that you should check out like Beetlejuice's Graveyard Review, the Horror Make-Up Show and Terminator 2 3-D.
The boys will enjoy the coasters while you can enjoy other things. I go every year and it is a lot of fun.
The Royal Pacific is the way to go if you have the money. The resort is as beautiful as any on Disney property and it has boats that take you back-and-forth from Citywalk and the parks every fifteen minutes. Second, you will get front of the line access to all of the rides. This will virtually remove the hassle of lines.
IOA is also experiencing construction problems with the development of the Harry Potter world.
As far as height goes, The Hulk and Dueling Dragons have the largest restrictions with 4 1/2 feet for each. I took my 7-year-old niece on all of the coasters at both parks and she loved it. However, if your daughter still has apprehensions there are ample calmer, yet still exciting, rides like Spider-man, Jurassic Park and Men in Black.
My opinion is that you should mix it up and stay at the Universal Resort. You will be pleasantly surprised.
WDW Thrills
Rock'n Coaster
Everest
Big Thunder
Space (CLOSED!)
Mission: SPACE
Kali River Rapids
Dinosaur
Test Track
Splash Mtn
Tower of Terror
UO Thrills
Mummy
Rip,Ride,Rockit
Disaster
Simpsons
MIB
Spider-Man
Hulk
DDFearfall
Ripsaw Falls
Popeye
Dueling Dragons
JP: the Ride
Jaws
Twister
Storm Force
Jimmy Neutron
Terminator 2
And Last But Not Least, Woody's Nuthouse coaster! :D
Universal Wins and yet only has 2 parks! Difinitely go to Universal if you have not been and stay on-site to get free Express passes!
While Disney might not have the rides, they have the resturants, shows, and rides overall. You can do everything at Universal in one day, but it takes four to do Disney still!
BTW, from the list above, Stormforce Accelatron (tea cups) and Dr. Doom's Fearfall (space shot) are fairly standard amusement park attractions and should not be a priority. Twister is a show not a ride and has just recently been reopened due to high volume crowds (meaning there's no telling if it will be open during your visit or not). Disaster and Terminator are shows as well (though Terminator is pretty thrilling), and Woody's Nuthouse Coaster is just for kids. If MIB is going to be on the list for Universal, then Buzz Lightyear and Toy Story Mania should be on the list for Disney - to be fair! And if water parks are part of the itinerary, Disney's two parks are superior to Wet N' Wild and/or Aquatica.
BTW, if you can fit it in the budget, check out the Blue Man Group at Citywalk...I think you will be pleasantly surprised.
Also, take the time to go to SeaWorld. Even if the Manta (the new coaster) is not open, it is a great park with some great shows, and a few (excellent) rides.
Raul brings up a good point: there is a ton of construction for the new Harry Potter expansion that will impact some sights and sounds at Islands of Adventure. So far, I think only one ride (a youth coaster called the Flying Unicorn) is closed down, but by the time April roles around there may be more impact. No word yet on any other closures.
I would submit that with all the new stuff Universal is planning, the VERY BEST time to visit would be mid to late 2010 after the new coaster, and the Harry Potter expansion are complete. However, there is still plenty to do without those attractions.
Additionally, there is nothing wrong with Disney for any age imho, but since you have gone every year, I certainly am all for you trying something new.
Note: If you decide to go to Disney, Space Mountain does not close until the later stages of April, probably after your visit.
Once you make a decision, let us know and we can help you with your touring plan!
