We have been to WDW 7 trips and Universal 3 trips (with a 4rth scheduled in two weeks). I am always surprised to hear people on this board rave about Disney relative to Universal-- Both parks are equally clean (in my experience), both have plenty of chipped paint and always a couple of attractions being refurbed. The customer service at both is wildly uneven-- some staff are wonderful, others utterly indifferent or downright rude.
I am also puzzled when I hear people say that Universal has nothing for young children-- our toddlers loved the "If I Ran the Zoo" and "Curious George" interactive playgrounds. They also worshipped Barney and enjoyed the whole Dr. Suess area (although the Cat in the Hat ride was too scary for our 3 year old).
Years ago, I think Disney had Universal beat from a customer service angle, but those days are looooong gone.
To me, the biggest difference is scale. Universal is truly a walkable experience. One can walk from the hotels into the parks, walk from one park to the other and walk to citywalk for a wider choice of restaurants or a movie. No buses needed. Because Disney is so much larger, transportation is unavoidable, But also because it is larger, one can spend more days there with more to do. A five day Universal ticket with a four night hotel stay is plenty for my family, while we can spend 7 nights at Disney.
The other difference is in hotel quality. The Universal hotels are Loews hotels and are beautifully run. Top notch service, very nice sheets, pillows, great house keeping. The Disney hotels can be beautiful (our favorite in the Animal Kingdom Lodge), but are mostly run like Holiday Inns.