As long as your joists are sized appropriately, it shouldn't make any difference. I'm assuming that you're doing the loading maths here. If you're just making modifications to a known design, you might want to get the final plans checked before you start cutting.
My house (still under construction) has off-centre summer beams (or an equivalent, not quite sure what the terminology should be) giving two different joist lengths. These beams line up with the divisions for the various rooms. The joists are all the same size (for aesthetic reasons) and are sized for the longest span.