I'm in a similar situation (except my trip isn't until October).
My plan is to go to Universal the first day because I think we can do most of what we really want to do in that amount of time. (Plus, we're staying on site so we'll have front of the line access.)
My second day, the full day, I plan to spend at IOA. I went there back in '99 and LOVED it, and we wished we had spent more time there.
Our third day, which will only be a partial day because we're heading over to Disney after check-out, we'll probably go back and cover anything we really want to do again. My plan is to get a pass where we can enter both parks on the same day, so if we decide to go to two parks in one day, it won't be a big deal.
BF and I like all the big rides, and we think IOA has more of the big rides with longer lines, so that's why we're going to Universal on our half-day.
Hope that helps!