I brought this up in my first impressions post a few days ago. I'm surprised nobody else brought this up until now. It's a problem, but i think it's something I can live with. I think the most ridiculous score I saw was Southern Miss beating Tulane like 93-0. You never saw that last year.
In fact, I remember an interview last year before NCAA '04 was released, one of the guys said that they redid the substitution AI so that when CPU teams get way ahead, they will sub in their scrubs and keep the final score reasonable. Maybe that somehow got changed this year.
Of course, that still doesn't explain some of the extremely high scoring, close games (provided they didn't go into OT)