So your boys will be 5 and 2 when you go?
We have three kids now, all boys, 8, 5 and 1, and we've done a bunch of amusement park vacations - WDW, Universal,
Disneyland, Busch Gardens/Water Country in Williamsburg, and Legoland CA.
Honestly, the height requirements create challenges at every park. For our older two boys, the more exciting the ride, the better. So they want to do whatever their height allows. My wife and I both enjoy roller coasters, etc., too. But this means a lot of rider swapping.
Rider swap at Disney (especially WDW) used to be great, but now it is the worst of any amusement park. Your 2-year-old will not be able to go into the queue with you, so you have to split up at the entrance to each ride. Then you get a rider swap pass that is only good for about an hour (they went from "good for a month" at WDW to "good for an hour"!) The returning party has to go back through the Fastpass line, which can often still take 15-20 minutes, plus the ride time. For stuff like Soarin' or Flight of Passage, the pre-show + ride experience can add another 15 minutes. So you can be looking at 30-35 minutes per ride, which means 60-70 minutes for both parties to ride - with Fastpass!! And for that entire time, the family is split up. The 5-year-old does get two rides, but it is still a drain on your day. Disney has also reduced/eliminated a lot of the in-park play areas and quiet areas that used to be good with toddlers. For example, we used to love Honey I Shrunk the Kids play area in HS, but they demolished that before building Galaxy's Edge. It used to be better at Disney than Universal, since you could get the swap pass, then go off and do something different with the toddler - but now the swap pass at Disney must be used almost immediately, so you can't go too far away, but you still have to split up = worst of all worlds.
Rider swap at Universal is pretty good. The whole party can stay together in the queue, and the queues are often very well-themed. At the biggest rides, there are nice areas for the non-riders, like a TV room for the non-riders at Harry Potter and the Forbidden Journey. Then you can do the swap and the second group rides almost immediately. So everybody only has to wait once, and the toddler will probably enjoy the queue.
So if the focus of your trip is the 5 year old, and they are at least 42 inches and like exciting rides, there will be a ton to do at Universal, and the 2-year-old will just get to tag along. Honestly, a 2-year-old will probably enjoy being carried for a bit and then walking through a castle (e.g., Harry Potter) as much as they will enjoy sitting on a boat ride (e.g., Pirates of the Caribbean).
With all that said -- you can check, there are very, very few rides that the 2-year-old will be able to do at Universal, and really there is not a single amazing ride with no height requirement. Whereas WDW has lots of fun, iconic rides with no height requirement - Kilimanjaro Safaris, Toy Story Mania, Frozen, Pirates, Jungle Cruise, etc.
Also, the water parks can be perfect in October, so it's worth considering -- Volcano Bay bizarrely has no family water rides, whereas the Disney water parks have a handful of family raft rides that would be fun with a brave two-year-old.