How do you plan to travel between the hotel and the parks? The walk from HRH is significantly easier than from the other hotels - but how is your older child at walking? Will you have a stroller at the hotel for transporting the younger one, or will someone be carrying her?
I remember waiting a long time at PBH for the boat - and the boat only gets you as far as City Walk; you still have to walk from there.
I remember being exhausted by the walk to/from RPR, but it was July so that could make a difference. Also, we were walking directly to the Harry Potter section of Islands of Adventure, and that's way in the back of the park.
If they will be swimming, look at pictures of the pools. My nephews did not enjoy the HRH pool. The big "feature" was supposed to be the underwater music, and they didn't care about that.
I like the atmosphere and decor at RPR better than PBH and HRH. PBH was fancier, but I personally don't feel it's worth it to pay more just for fancier. You are supposed to be impressed by the rock memorabilia at HRH, but we weren't.
My take on it is that all of the hotels are kid-friendly, but the decor at HRH and PBH are not designed to impress kids. Your kids would be comfortable and would have a great time at any of the hotels, but wouldn't appreciate the design for which these two hotels are known. If you were to point out the design features at HRH or PBH to your kids, I can imagine them saying, "Who cares about that?" (to quote one of my nephews, who was not talking about hotels at the time, but I love that line.) I think they would appreciate the decor at RPR.