Maybe that's why so many of my favorite things have identifiable flaws. It was the processes of accepting a work beyond its inherent flaws where I really found enjoyment. Final Fantasy VIII, Pain of Salvation (band), Cryptonomicon (novel)... all examples of some of my favorite works, and all of them have very apparent flaws that took time for me to overcome.
Sometimes it takes awhile for a game/album/movie/book/whatever to click with me. But generally, for me, that's not a case of looking past its inherent flaws, but just... Well, okay, sometimes things are just really detailed and it's hard to get the underlying gestalt unless you spend some time with it. That's not looking past flaws, though -- just spending some time wrapping your head around it.
On some cases I HAVE had to look past flaws to enjoy something, but usually that's a matter of finding out that something I perceived as a big problem really wasn't that big of a deal after all. For instance, the features they cut from X-Com: Apocalypse used to bug me, but looking back I don't think they would've added much anyway. Although more often in cases like this I look back and realize the perceived flaws weren't really harming the product anyway.
However, every time I've actually had to *work* past flaws, especially ones that are pretty non-trivial -- in cases like Legend of Mana, FFVIII, Wizardry 8, or a lot of other JRPGs and WRPGs that have gameplay mechanics that are essentially broken and badly designed to their cores -- I end up realizing that there was just something about the game's aesthetics, story, charminess, modus operandi (In cases like Daggerfall or Space Empires 4 where I was, once, more in love with the idea of the game than the game itself), or whatever that I liked, and so I was willingly ignoring the fact that I wasn't having fun at all just so that I could latch onto these periphery things.
I could sustain that when I was younger, which is why I used to care about things like story and art design and companies experimenting. Now that my attention span isn't as bulletproof as it used to be, I sort of can't keep that up*.
* in this sense, I think I WAS having fun with Disciples 2, or what I played of it, but I also had a niggling feeling that it'd get, eventually, grindy and sloggy. Similarly, with Suikoden recently, I wasn't actually disliking what I'd seen, but it really felt like the game wouldn't ever go anywhere. At least in the latter case, I'm probably right. In the former case, most of the stuff I know about Disciples 2's later stages in the campaign are coming from the sort of dumbasses that liked HoMM2 *a lot* more than HoMM3 even though they're the same damn game, so who the hell do I even trust there!
** You can make any videogame look terrible by recording yourself playing it on easy without understanding the mechanics, making fun of everything in it, and then uploading this video to youtube. *EVERY* game.
*** I'm also not really sure the "Paradox of Hedonism" work here since that looks like it's referring more to personal happiness then fun. Playing other peoples' games is never going to make me happy. You can't really seek personal fulfillment from gaming, and if you do, you'll just end up pissed off (and that bit there DOES work with the Paradox of Hedonism, I'd think -- trying to use games as a means to achieve happiness. It just doesn't work on an individual is-this-game-fun-or-not level).