We've done both locations. We tend to prioritize WDW, and do more days there.
I can't speak for others...but it's hard to talk about either without a few tiny comparisons. For us- the new HP excepting- Universal has some of the top rides, but WDW was more comprehensive. I think Three Broomsticks is amazing, probably better than any QS at WDW, but I like seeing the different parts of WDW on most visits- so the Bwk area, at least one monorail resort, the WS. When it comes to dining - for us- we're just not as nostalgic for US dining. It's hard to explain why.
But that's the past.
The new HP/Simpsons areas, combined with WDW's meaner policies/high prices, is tipping US into more of a must do part of our vacation. I never thought I'd say that! Suffice it to say, Disney's kind of driving us away, while Universal's adding appeal. I feel like Disney has taken several measures to punish guests, and that's not a magical way to be treated.
What works for us is to make sure we have a car.
It also pays to pack with a split stay in mind. I don't fully unpack anywhere, and try - at least the second half - to leave some stuff in the car. I put my toiletries in 3gallon zip lock bags (dump n GO), but travel carriers might also work. IMO, they always have too many small pouches.
Also, we do better when there is a reasonably clear division of labor. One person packs most the luggage, so they know everything was packed, and where it is. Meanwhile- the other person gets the more random honey-do list: reviewing plans, getting the car, double checking under the bed, etc. If the packer makes a request, the honey-do person tries to help.
It doesn't always work perfectly, but assigning roles helps us stay organized, which is key to easy split stays.
One more thing worth mentioning...there's much more to FL than the two theme parks! Sometimes on transition days eating offsite is nice, or going someplace else. We've recently discovered Tampa! St. Augustine is also amazing! the Everglades are pretty far, but also a big wow! Stepping outside the themed bubble is great place to find fresh air!
But it gives me plenty of time to keep an eye on all the discounts. I signed up for emails from Universal too, so hopefully they send out discount emails too...
I will do well to even drag my sleepy-head self over if I am staying onsite. So I will lose a day or at least half a day in the move. Mid-trip that wouldn't be bad. The crowd calendars all recommend doing USF/IOA mid-week so that would lend itself to just staying put at the resort and commuting. I could also just do a car rental for two days then and ride ME both ways.
I'm so shocked! Normally, he's not a move from here to there kind of guy, but what sold him was the "avoid the lines" when you stay at one of the 3 Universal resorts. I'm not kidding, the man was giddy with excitement! 
He's so excited for the fast / daredevil rides and for HP also.
I'm so excited to do a split vacation now!
