Personally I thought the Rupee thing was annoying. Putting them back in the chests, while helpful when you needed them to buy rediculously overpriced things *cough*cough* it was annoying when you had to return to a dungeon and were looking for the small key you missed and all the chests you put back were still on your compass. I think they should have erased those chests from your compass, maybe just for that visit to the temple.
P.S. I didn't think the swimming controls were too hard, but i did think switching tunics on the fly under water did make things awkward