A lot depends on water levels. Yampa can be epic, big water or low water as it is natural flow - I have seen it at 6k, 12k and 17k all in the same time frame but different years. Lodore is basically dam controlled and if you get 2000 cfs my opinion, that is big water for that run. Lodore is fun at any level as far as the rapids go.
Both come together at Steamboat Rock so you get two days on the same river regardless of the permit. Last day thru Split Mountain (again depending on water level) is a bang up ending to the trip with big western river rapids giving a great ride.
Yampa has a couple of bigger rapids which on low water is not much. Warm Springs at hi water is short but powerful. Camping just below the Warm Springs rapid up on the hill is about as good as it gets any where on any western river as far as scenery and there is a nice little creek there for shower water. My opinion, Yampa has the best red rock canyon scenery with a couple days of bend your head back and stare at the steep multi colored formations. Great camping along the way with Harding Hole being a great layover camps with a hike and steep cliffs.
Lodore to me is more creek like. Lot more smaller but requires maneuvering to get down drops. For rapids I enjoy Lodore more. Scenery tho is very nice but nothing like the towering cliff faces you see on Yampa. Camps are ok, but again my opinion, a step below Yampa.
Last day of both runs, has a few miles of slow water just before Split Mountain gets it on.
Also camping below the last nice camp at Jones Hole can be exciting bug wise until you hit Split Mountain.
Whitewater Rafting Campsites | Resources for Planning Rafting Trips
For a good idea of both runs, rapids, camp sites and scenery.
Bottom line, you cannot go wrong on either trip. Just a different beginning to the same ending.