If possible please try and spend 2 full days one for each park to get the full experience. I dont think you will be disappointed. I also dont think you will have a lack of things to do and see with a 3 1/2 year old.
My first family trip to IOA/Universal my kids were 3 and 7. This trip was a combined Disney- Universal trip. My thinking was the kids were going to love Disney and my husband and I would get more out of Universal. That didnt end up being the case.
Here is what my family enjoys at both parks and what the kids really love.
Universal:
First let me start by saying Universal Studios offers more attractions the whole family can enjoy together.
Production Central-
Hanna Barbera really cute both kids loved it...if you think its too intense ask for a stationary car.
Nick Studios- Great for the whole family.
I would skip Alfred Hitchcock with your child and do it alone if possible.
New York-
Twister...do it alone again too intense for many 3 year olds my 3 year old did do it didnt like it but when we returned this year (at 4) he enjoyed it!
Konfrontation...depends on your child again may wanna check it out first before deciding. My 4 year old loves this ride and teases King all through it.
Blues Brothers show- good for whole family.
San Fran/Amity-
Earthquake...loved it at 4 was frightened at 3. Could also be comfort comes after a few experiences and starting to know the difference with real and fake.
Beetlejuices Revue...whole family loved this show.
Hollywood-
No go with the make up show but do try and see it for yourself.
Terminator2- Too intense for my little guy. My 8 year olds favorite though.
Lucy- fine for whole family.
Woody WoodPeckers KidZone-
Kids LOVED this entire section! Not to mention the adults as well really a wonderful section and can spend way too much time here having a ball!
Animal Actor Stage- Great show kids really enjoyed the animals.
A day in the park with Barney- Okay I really tried to not to have to do this one but kids insisted and I am glad they did! We all enjoyed it a lot.
Curious George- Most time spent in one area! Be sure to travel behind the water section to the balls! what a blast
It is an interactive playground for all ages.
Woodys Nuthouse coaster...great coaster for a 3 year old. Really cute theme.
Fievels playland...wonderful for small children even a special section just for the very little ones.
ET Adventure- Great for the whole family.
Also watch for many character interventions in this area!
World Expo-
MIB...my sone loved it at 3 and its his favorite ride now. whole family experience for sure...make sure you look at the pictures on the way out. Lots of fun.
Back to the Future- wouldnt take a 3 year old on this one but try and do it alone in the front seat.
Islands Of Adventure:
More thrilling rides but just as many kids areas and lots of fun colorful sights to enjoy.
Toon Lagon-
Dudley do rights have to be 44" my 4 year old still isnt interested.Great water ride big drop
Popeye bilge rat barges-
48" height require. although they must have lowerd that cause we all did it as a family many times this past september. You will get very wet but its great fun.
Me Ship Olive-kids love it! They can also blast the people on the Barges as they go by from here. (one of my favorite things to do)
Jurrassic Park-
Discovery Center- Great for the whole family...make sure you try and catch a raptor egg hatching.
Triceratops Center- Great for the whoel family.
Jurrassic Park river adventure- 42" height requirement. We all love this ride.
Pteranodon Flyers- well here opinions vary. This scared the heck out of me. Kids liked it fine! You cant ride w/o a kid!
Camp Jurrasic...cool playground worth checking out.
The Lost Continent-
My favorite Island!
Poseidons Fury- dark and loud at times but wonderful show (my opinion) may want to see it yourself first to decide if your child will like this one.
The Mystic Fountain- My most favorite attraction that I can wipe out most my day at. We have had more family memories here than anywhere else. Make sure you throw in a coin and make a wish.
Sinbad show- Great for whole family very entertaining.
Dueling Dragons..Coaster's (2)
No good for little ones.
The Flying Unicorn- 36"...my kids love it but I cant ride it they have to do it with Dad. They ask to do this one over and over again.
Marvel Super Hero Island-
Spiderman...Just awesome!!! First time through when my son was 3 he had to close his eyes. He was frightened. Now he loves it...just depends on the child.
Dr Doom...no good for kids. (small one anyway)
Storm Force- Havent had any desire to even try this one.
Hulk...great Coaster very smooth, not for small ones.
This is another area to be on the look out for characters and a mini parade of villans and superheros!
Seuss Landing-
Great spot for the whole family! So colorful and lots of interactive play for kids.
If I ran the zoo...lots of fun
The Cat in the Hat- if spinning is a problem ask the attendant to turn off the spinning for your couch. My kids really enjoy this ride a lot. I do too.
One Fish Two Fish- Kids love this! Reminds me of dumbo with water options! lol
Caro Seussssss-el
Merry go round...really cute colorful creatures! Look for the switches/buttons that make each one move while you ride.
Do try and get over to the hotels maybe have a meal at one...very pretty settings and some great restaurants. City Walk also has a great water display mid section that my kids love to frolic in!
Hope you have a great trip