I never really thought of it much, never really annoyed me. There are many different devices for framing and constructing a narrative. It's hard to say that one device is inherently bad. It's all about how well that devices is utilized. There are some narrative devices that could be considered overused, or copouts that avoid deeper storytelling, but that only really applies if it's not done well or ruins the pacing (another problem that can arise from temporal narrative devices). However, some are used to great effect. As much as I have my problems with FFX, the way they framed it as a story told from a point about 3/4 the way through the game was very effective.
I dunno, the more I think about it, the less examples I can think of when flashback scenes really annoyed me. So many games are temporally linear that it's kind of refreshing when a game breaks form. I actually thought it was one of the stronger aspects of FF7 (even if the first Tifa scene was pretty cheesy), and even better in FF8.
But then again, I'm pretty open to a lot of narrative devices. I don't even mind long cutscene sections, as long as they're done well. Some complain about having their game hijacked by cutscenes, but to me, that's not so much of a problem, unless the cutscenes are bad or uninteresting.