Sounds like the northern loop will be during the summer, so everything is open. With three months, you can actually do justice to a lot of places. (Often, I'll see a post where someone wants to do this in two weeks!)
After Yellowstone and GTNP, I'd head north to Glacier NP. Then work your way to the Seattle area, passing through North Cascades NP. (If you have time and desire, another way to go is north into Canada, visiting Banff, Jasper, etc. before heading west on the Trans-Canada Highway, re-entering the US somewhere north of Seattle. This is an unbelievably gorgeous trip.)
From there, spend a few days exploring the San Juan Islands. Then hit Olympic NP before heading south to Portland, visiting Mt. Rainier and Mt. St. Helens along the way. The Columbia River Gorge above Portland is worth a day or two of exploration before you head to the coast and take US 101 south all the way along the OR coast. Oregon SP's are the best. Do head inland to explore Crater Lake. In CA, I'd continue on down the coast maybe down to Bodega Bay before heading inland to explore Lake Tahoe, Yosemite, Sequoia, Kings Canyon, etc. Then it's off to LA. I'd store the RV someplace rather than try to navigate SOCal traffic.
Don't worry about the mountains. You'll be in the company of thousands of RV's travelling these same routes. Going downhill, use your tranny rather than your brakes.
