There are very few quests that I do specifically for the rewards, so I've never really noticed or paid attention to the quality of the reward as compared to the difficulty of the task. For things like the Golden Skulltulas or the Poes, yes, the unlimited money is pretty pointless, but after getting all the good rewards I wasn't doing it for the money anymore. These completion quests can only be finished near the end of the game, so at that point there isn't anything worth getting other than self satisfaction at having completed the game, and since it is a game, I find that to be enough. I mean, that's the point of a game, having fun. I think part of the reason for the more worthless endquest rewards is because the satisfaction of finishing is good enough in itself, or maybe that's just me.
However, if the series made greater use of game mechanisms like second quests, there would be so much more potential for good rewards, namely unlockables for the second playthrough. I know that was a huge motivation for me when I was doing the really hard quests in Okami.