I've done several variations of trips through the SW National Parks in the last couple of years and here are my lodging recommendations:
For Bryce lodging, I've stayed at both Ruby's and the National park lodge; the latter wins hands down. The ability to walk out your door to the rim to catch the sunrise/sunset, to stop off in your room mid-hike, etc is wonderful. You are in the trees right on the rim for a true National park experience. With Ruby's (or their new one across the street) you are in a big complex with the bus tours, shopping/restaurant complex. With Bryce, I think it is worth the extra effort and cost to stay in the park.
For Zion: The lodge is in the middle of the valley and you can walk out your door and pick up a trail or hop the shuttle bus (if it's running) to trails further along the road. Springdale is very close and also pretty convenient with the shuttle bus extending into town. I would definitely do the lodge in Bryce, but go with whichever motel in Springdale or the lodge works out best for your pocketbook.
North Rim Grand Canyon is far enough from any nearby lodging that the lodge definitely wins hands down. However, it closes up in mid-Oct and opens in mid May so the timing has to be right.
About a half hour from Bryce is Kodachrome Basin State Park which has some great little cabins right in the park. They just changed ownership but are a great deal. The cost was about $100/night for a cabin with 2 beds, micro/fridge, picnic table on the porch and barbecue outside. We walked from the cabin to the trails etc. I really liked them for comfort and ambiance (and the sunset from the porch was fabulous). Kodachrome SP is a good base to explore the west side of Grand Staircase-Escalante National Monument.
For Capitol Reef National Park, the best place is Torrey, Utah and Austins Chuckwagon motel with regular motel rooms, 2-BR cabins with micro and large fridge, and a 3-BR apartment over the store/bakery.
In Moab, check out Accommodations Unlimited for some condo rentals. Excellent service and excellent selection of some very nice condos. There was a group of us splitting the cost so it turned out to be less money than the motels.
Sue