just got back from 3/8-3/12 vacation. stayed at HRH and FOTL was worth every penny. It was spring break for colleges, private schools and local schools, so the parks were pretty crowded. We were a group of 3 families (3 sisters) with kids 6,7,8 yo and teens 13, 18, 19 yo.
Our younger kids loved IOA, especially spiderman. I don't know whether your 3 yo would make some of the height requirements but he could see the shows in the Lost Continent (Sinbad and Posiedon), Suessland (they loved the 1 fish,2 fish ride), Comic land and Jurassic park (pterdactyl and nursery). The older kids will enjoy flying unicorns and other "big" kid rides. If you anticipate any crowds (and they are worse in the morning than late afternoon), I highly recommend taking advantage of fastpass or even better, stay onsite for FOTL or VIP tour.
We visited Magic Kingdom on Sunday (supposedly a slower day) and it was mobbed. WDW only allows one fastpass per time, so we waited for space mountain for over an hour and then made buzz lightyear fastpass time. Did the same with splash mountain and runaway train. It was no comparison with FOTL at USF/IOA which made the trip so enjoyable. But even without FOTL, USF/IOA allows for multiple fast passes at a time which makes waiting manageable.
Another fun part of IOA are the games. My brother-in-law a giant stuffed bulbasaur(pokemon character) with a ring toss game. He got a big bucket of rings for $5 and kept tossing to one sword. He only went through one-third of the bucket before he won. It was so big that my 6yo nephew had a hard time putting his arms around it.
USF has plenty to see and do too - but you're 3yo will be able to participate more at IOA just for it's visualness and playful theming.