This topic has been really interesting so far. I understand both sides of the argument, and believe it or not, organman88 and others have hit on some very valid points.
I think the problem/divide comes in with how each person interprets and uses the number system. Using it based off its original intent or based off something you've created makes all the difference in the world; especially when there are others trying to learn from you.
The original intent of using the number system takes into account that you are following the basic "rules" of theory, using the chords built off the scale degrees. If the chord is major in the scale, then it's going to keep it's major base. Plus, the root will be whatever scale degree you're on. For example, using the number 1 (I) implies that the chord is major and that the 1 is in the bass. Even if the chord is a major 7, major 9, dom7, dom13th, etc. the base of the chord is still major. Using the number 1 (i) implies that the chord is minor and that the 1 is in the bass. Even if the chord is a minor 7, minor 9, min 11th, etc. the base of the chord is still minor. etc....
My approach to the number system is a little different and "bends" those rules a little, lol. I see the numbers purely as bass notes, then I leave room for the musician to decide what chord to put there. Also, I use the major scale as my reference for the bass notes. So, if the song is in a minor key, I think about the music using the relative major key. All my minor 1's I see as 6's. This approach takes into account that you've done the work already at having options for each bass note. In this case, you're not "limited" to only using the scale degree chords, you can pull chords from other places, but still fit the song and stay in key.
See what I mean? Same number system, different approach, different results with each approach. Other musicians may also have their own ways of interpreting and using the number system, this is my way. It's not the only way, but it is a way to look at it.
In the end, whatever approach helps you get better as a musician is fine. Not everyone will agree or understand, but if it works for you, keep using it. Just don't automatically disregard another musician's approach as wrong based solely on your knowledge as being the "end all, be all" of music. I've fallen into that way of thinking b4 and am working to not fall in it ever again.
God bless!!!