I find ST to be really boring and have been campaigning for it to be shortened, or made more relevant, for a while.
In my experience though, there are no ill effects from resting your fully developed ML players most (if not all) of ST. I give my ML vets very, very little playing time in ST.
ST does, however, give you the chance to get your prospects extra playing time (and therefore, theoretically, extra development) with your ML level coaches. That is the only useful thing I'm aware of regarding ST, getting your prospects a little extra field time to develop with what are, hopefully, your organization's best coaches.