What about weather? Can it be a factor in a decision which way we take the loop? Is there any possibility for waterfalls to still flow in Yosemite in late June? ]
The waterfalls usually flow through June and peak flow is usually in May with the snow melt but the Sierra's have had a lack of snow in recent years which could be a factor.

I've been looking at Bryce Canyon and Capitol Reef the whole time but can't decide if it's a good idea (and how to) to include them in the itinerary.
You could have another month and wouldn't be able to fit everything in, so unfortunately you have to pick and choose. We all start out with way to much and then have to cut back, but it's always a great excuse for another trip !