Alternate D?

So, working my way slowly through the 5-chord power pack and changing chords in rythm, one thing I've run up against is that the proper fretting for D just gives me fits. I cannot get a consistent clear tone and switching to/from D is a labor.

I find it much easier if I reverse my index and middle fingers. Index on the 1st string, middle finger on the 3rd string. Am I going to run into trouble later on if I learn it that way? Is there some common change to/from D that is going to be more difficult than if I learn it the traditional way?

I guess the short answer from my perspective is whatever makes it work for you, but it's pretty uncomfortable for me when I try it. The conventional method will come around with practice.