I usually do the Spirit Temple first, because of the fact that I was so afraid of the Shadow Temple and Bottom of the Well levels. I believe that I also got through the Haunted Wasteland without the Lens of Truth, using some kind of guide that walked me through it in painstaking detail.
I personally think that the reason that rupee is so hard to get, is because it was meant to be a bit more challenging to reach. The Hover Boots make it easy, but I don't think it was meant to be that easy originally. They might have just moved the Shadow Temple before the Spirit Temple because they realized people might have too much trouble solving that puzzle without Hover Boots.
In any case, I would say that the Spirit Temple was originally intended to be before the Shadow Temple, and can still be done before it... but the game now expects you to do the Shadow Temple first, as you usually have to get the Lens of Truth to cross the Wasteland anyway, and the Shadow Temple is right there.
I've beaten the game both ways, though... and I think that beating the Spirit Temple last IS a bit more satisfying, because of all the cutscenes and such in there.