This has been a sore spot of mine for a long time too... but in the end I think I'm able to see the 'greater good' of the decision to not put two drives in the machine. What doesn't make sense to me is why Apple chose to add metal to the framing preventing another drive from being inserted in the second bay.
Apple is known for their forward thinking, so it doesn't stack up to see them preventing such a thing. Obviously enough people were wanting to add the second drive and did so by hacking their computers.
I have a G5 -- which only has room for one drive as well. I don't really miss the second drive, but at times I suppose it would be nice to have one. Kind of the two button mouse argument I guess.