we took our ds who was 4 back in 2005. he loved it. Suess landing at IOA is good for kids. We did 1 day in each park. he enjoyed them both. The only negative thing was when he was REALLY dissapointed that he was too short for jurassic park.
The one thing that Universal has over Disney is their parent swap facility. at US/IOA one parent joins the regular queue line, the other goes up the exit ramp with child/children and waits in a waiting room. most have tv and toys to keep them entertained. then when parent 1 comes off, parent 2 goes to the exit platform and gets straight on (no waiting around in FP lines). this will save you time if you like the bigger rides that the kids are too small for. If you go to universals website you can find all the height requirements and plan accordingly. Your ds and eldest dd will probably get on most things.
like Disney there are lots of Characters about, so make sure you bring your autograph book.
We are also going in Sept and will have a 2yr old with us, and plan to do both US and IOA with him. With the light crowds i've heard about in Sept, i dont think we'll have any probs (hopefully).
thinking back, i think the only rides my ds couldn't do (and he's short for his age) were;
at US: men in black
at IOA: hulk, duelling dragons, fearfall, ripsaw falls, blutos barges? and possibly storm? He was just 40" at the time.
there is more for the younger ones at US, but enough to keep them entertained at IOA while the grownups have fun
Ds's favourites were Spiderman 3d, Cat in the hat story-acted out by characters (IOA), Shrek 4d ,ET, curious george 'WET' playground, Barney show (US) He also like the Blues Brothers Show - but didn't like mummy and Daddy dacing along

and Beetlejuice graveyard revenue (which contained loud pyrotechnics at the start).
As i stated earlier, we went in 2005, so i dont know whats changed since then, but travelling with younger ones certainly won't put me off. Whatever you decide, i hope you have lots of fun.....