I used to go all flat front w/ no cuffs. I still do that for non-business pants (wool or cotton). But lately I haven't minded picking up some pleated and cuffed dress pants for work. You can find better quality for cheaper (thanks to the flat front craze), and I prefer suit pants to have pleats (just a personal preference) so I figured why not dress pants? That said, I think it would be a mistake to just load up on pleated pants. Why not have a nice mix? FWIW, in my opinion cotton pants shoudl always be flat front -- cotton pleats just don't drape well at all, whereas wool pleats can drape very well.
I'd say it depends on your size and shape. For example, pleats look terrible on me (6'0, 175#, 32/33 pants), except on very dark pants where they are not noticeable, while flat fronts look terrible on many people, but great on others. I agree that most cotton pants should not have pleats. I have seen it done well, but not often.
I perfer my suit pants to have pleats and cuffs in them. To me it just looks better. If i'm just doing something casual then i perfer the pants to be flat front. I agree with johnny that a nice mix is a good idea. Variety is the spice of life. As for the cotton pants with pleat i fully agree that they should always be flat front. I bought a pair with pleats and well i hate them and they are sitting in my closet and haven't been touched in a year or two. nik