IC vs. discrete
The PCB for the IC version is likely a heckuva lot easier to design than will one for the discrete version. An IC version will ususally be more reliable in the long run. If you buy the parts new (vs. using the discrete parts from your junkbox), the IC version is usually lower in cost. IC versions of may circuits (not necessarily stepper controllers) often incorporate nifty extras like over-current protection. The IC version will usually be easier to implement, being more of a "black box" that you simply feed signals to make things work right the first time. The IC version will likely be more balanced and allow smoother motor operation. The IC version will be a proven design with lots of hours of R&D behind it while the discrete design may not -- they don't go into IC production with a possible lemon if they can help it. It's easier to heat-sink an IC than it is a bunch of transistors, especially of their collectors are at opposite potentials. After you design and build the boards, the IC version will probably work OK and you'll have some troubleshooting to do on the discrete version. In otherwords, why build a discrete op amp that will be flawed when you could use a simple 741 jellybean to do the job?
Dean