I play RPGs for the most part, so a cookie-cutter plot will pretty much put me off from the outset. But, honestly, that still will not prevent me from at least giving it a try, with the hope that there are some pretty damn good plot-twists coming my way, or at least a fresh take on an old story.
Overacting, Bad script (which, contrary to what some believe, is not the same as overacting), flat characters, uninspired locales, lame villains (this goes with flat characters), and annoying fairy creatures are also things that irk me some.
But besides plot, I'd have to say lack of attention to background is something that annoys me a bit, especially in RPGs, where walking around vast areas is a pretty much a given (although I am not limiting this to just RPGs, any genre can have plain backdrops). I seem to notice it more in cel-shaded games like Dragon Quest VIII, Eternal Sonata, Tales of Symphonia, that new Naruto game for the 360, and Wind Waker, but it also shows up in plenty of other RPGs, including, but not limited to, Final Fantasy, Star Ocean, Xenosaga, etc. It's not that it really puts me off from playing the game - it's more like a distraction in which I stop whatever I am doing and begin to compare the level of detail on character models to the level of detail in a castle, or a cottage, or even a TREE.
So unequal level of detail from character models to backdrops, bad graphics in general, exceedingly steep learning curve (every Capcom and SNK game I have ever played comes to mind) un-involved gameplay (where one button pretty much does all the work for you, although there were some "button mashers" I had a blast with), bad camera and bad camera angles; annoying music, battle cry, victory cry, etc.