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The Gen4 has some nice new-to-Glock features, like a reversible magazine catch (for left-handed use) and replaceable frame backstraps for different size hands, but it also has had a few reports of functioning problems; enough reports that Glock has addressed them by providing replacement springs to solve the problems. The Gen3 guns have been around long enough to have a fantastic reputation for reliability, and unless you absolutely can't live without one of the features on the new Gen4s, then I'd recommend you get a Gen3.
Full disclosure: I'm not a Glock employee, nor do I sell Glocks, but I really like Glock 9mms. Here are some of mine (all Gen3 except the Gen1 longslide G17L on the right):