We've done this three times now (split stay). Once off-site for the Universal part, twice at Royal Pacific. Once at the beginning of the trip, twice at the end.
I will concur with the other poster who declined to start the debate over whether Universal is better, but I will say it's different.
There are good differences that are quite enjoyable, and they are magnified by staying on-site. The unlimited fast pass that come with an on site stay (at the more upscale Universal resorts) is fantastic.
I think it's especially fun if the Universal trip happens at the end. It feels like a vacation from the rest of the vacation. Even though I like FP+, I found that I really loved having the unlimited express pass at Universal after a week at DW, and all of the planning, appointments, and reservations that now entails. At times we were almost giddy -- we could go on any ride at any time and walk to the front of the line! Spontaneity! Woo hoo! My kids did the Hippogryph 6 times in a row in fast succession.
For the few attractions w/o the unlimited express pass, I find the single rider lines work just as well.
(Yes, I like FP+. but let's not go there either! Point being if you don't like FP+, then you'll probably appreciate unlimited express even more).
Finally, I really like Loews hotels -- the onsite at Universal. I love staying on Disney property too, but there I feel like I'm paying more for Disney magic and convenience. At the Loews resorts, I feel like I'm getting just a little bit more service and amenities in line with the price.