The only thing I have noticed is that there are more penalties for some reason. Typically Holding and Clipping. I don't quite understand how the slower speed could affect penalties, but I'm definitely seeing about 3 more penalties a game on the slower setting. Seems strange. It might just be coincidence, so I'm not sure how much weight you can put into it.
On the slider settings I have been working on that give some pretty darn realistic stats for teams and a challenging game as well (especially if you take the 'Madden Challenge') I haven't noticed much of a change in game play when going from Slow to Very Slow. Just better animations!