You know, I bought a bike about 2 months ago and had a similar experience to einsteinjb's. My LBS told me that the 21" was the way to go. I'm 6'1 190lbs, 33in inseam. They told me that on the 19.5" my knees came too close to the handlebars and recommended the 21". I felt the same discomfort as my crotch was right up against the bar. I got on the 19.5" at my request and personally in riding them both just felt a little better on the 19.5" so I bought it, and to their total defense they said that it's not TOO small, just that they felt I'd be better on the 21".
The LBS told me that the 3-4" of clearance is the old school means of measurement and was from the days before suspension forks and the newer MTB geomertries. Dunno if it's true, but I'm pretty happy with my LBS.
My only concern is that their recommendation planted a doubt seed in my mind. I worry that in order to feel comfortable that I sit too far back on the seat. To be completely honest, the front of the seat causes a little discomfort for my twins down low if I don't adjust my seated position JUST right. Is this as I fear a top tube length too short, would another seat fix the problem, or do I just need to learn to STFU and deal with it? I've only got about 200mi on the bike so far so I'm definitely interested in your input. THANKS!