I think propensity for Delayed Onset Muscle Soreness (DOMS) must be genetic or something because I've never been able to get "past it," even after many years.
Have you tried avoiding eccentric exercises? The ones that require you to stretch? Try to do more of the "push-style" exercises.
Also, I highly recommend getting a physiotherapy-educated trainer for at least several sessions. They know _exactly_ how to make people hurt after exercises :)
