The only "Bad" aftermarket seal I've had was the boot lid (on an 86 560SL). The others worked well, even the infamous pillar post seal. The price difference is significant.

I think part of the bad rap is that when a car gets old, the adjustments go out of whack but the original seals bend and conform to the misadjustments. You put in new seals, and they seem like they don't fit. The top of my 560 is full of subtle window-top and boot lid adjustments.