Great points. In our own work in Colorado waters, there is so much stocking that genetic issues cannot be ruled out as a potential confounding factor. All the waters studied in Colorado are subject to heavy stocking (usually annually) and potential genetic effects.http://afs.tandfonline.com/doi/abs/10.1577/1548-8659(1979)108<277:EOSOGO>2.0.CO;2
Have you considered the effects of stocking on genetics? I have a casual acquaintance with some fisheries folks here in NM, and they believe that because they have to keep re-stocking, they are engendering all kinds of changes, side effects if you like, to existing populations. Gene pool changes are one of those they are concerned about. So what you saw in terms of lentic ( populations that cannot move far over generations/lifetimes compared to semi-anadromous (Coastal cuthroat trout) populations for example) may be related to other kinds of changes rather than competition.