First I would say: If you post this question on the Universal/IOA board, you will get totally different answers. I would thoroughly research both, and see what you think your family would most enjoy. WDWs prices are much more than Universals, but if you did split, would you then buy 2 1 Day, 1 park passes for Disney, or would you buy 4 day hoppers AND Universal tickets, then save the other days on your hoppers? That may influence your decision. Also, if you think you would be able to come back in the near future, I would probably just do WDW and save US/IOA for next time, just for the fact that you CANNOT see even half of Disney in 2 days.
That said, although it's true that US/IOA once were mainly for older kids and adults, there is now alot for little ones. You don't say when you are going, but US has 2 new attractions opening soon: Shrek 4D and Jimmy Neutron. They also have Nickelodeon Studios. IOA has Seussland, which is completely geared toward little ones. Plus, I think the older one would really enjoy ALL of these 2 parks. So if this is like a once in a lifetime (or once in a decade) type trip, I would try to split and do both. Lastly, if you do split, I would spend the 2 WDW days at MK and MGM, where there are enough attractions for both age groups.