Alignment of rafters and joists is more of a constructability issue than anything else. Alignment of rafters over the ridge makes it easier to install purlins and sheathing. Also this would lead to uniform spacing at the gabel ends of the building. If the roof framing is exposed, you also have improved aesthetics. The same advantages apply to floor framing.

I agree with Jim. Unless you have some really good reason for doing otherwise, you are best to follow convention. If you want to do something unusual, you should have your plan reviewed by someone with enough experience to know the potential risks of your choices.