First, the pools. Would you and your family prefer a slide or a water play area? The HRH pool has a slide, RPR's doesn't. But RPR's has an interactive water play area. When my kids were younger, they really liked that better than a slide. The HRH rooms will be a bit bigger than the RPR rooms (which can sometimes feel a bit cramped.) I prefer the selection of restaurants at the RPR (especially the Sushi.) In general, rooms at RPR will be slightly less expensive than HRH rooms (but on any give set of dates that may not always be true.) Would you prefer a South Pacific/Polynesian theme or a Rock Music/Party theme?
Personally, the walking distance from either hotel to either park isn't large enough to be an issue. So that has had little to no basis on our decision. We've stayed many more times at the RPR than we have at the HRH over the years as we just liked RPR better.