There is some pretty bad blood between the Shadowrun edition camps. From what I could pierce together it has more to do with CGL as publisher and some shady deals that happened when they took over. But its hard to get unbiased specifics about that.
Also, many of the older players (or the ones already seeing CGL negatively) complain about story retcons and "turning Shadowrun into D&D"
More so with the later then the former. Having to do with embezelling funds, unpaid freelancers and bad blood that stemmed from it. Less to do with rules changes unlike the 3.x vs 4e
5th looks pretty ok from a rules standpoint. Fluff stand point there are vexing retconns and other items from fluff changes and story movements.