My top Five

Fallout 3 - As has been mentioned already, Fallout 3's main plot is a bit of a disjointed mess with predictable payoffs for the obvious setups and hampered by scenarios that don't actually add to the world or story. I actually skipped several of the story missions because I found good old dad wandering the wastelands long before I found Three Dog. The game's original ending is also just a plot hole with my character valiantly sacrificing their life for the Wasteland by radiation poisoning despite having two party members who literally eat radiation standing right next to me. Even the writing of the story is pretty awful once you get past the Vault 101 stuff. What makes this really annoying is that there are some actual good characters and stories in this game, they just all happen to be optional.

Final Fantasy Tactics A2 - Like Fallout 3, TA2 actually has some great characters and scenarios, they're just all optional and have no connection to the main story. What constitutes as the main story is absolute garbage. The plot points are thinly connected and serve more to open up the world (and the better side stories) than actually being some intelligible narrative with a good arc. The main villain has no purpose in the story and little background to flesh her out, the final boss is such a Space Flea from Outer Space, he makes Necron look like a full fledged character with purpose and the plot is the flimsiest of excuse plots. What is most insulting is how FFTactics and Tactics Advance actually had gripping philosophical narratives that dealt with moral issues whereas Luso is just some vapid child having adventures in Ivalicland while putting off his need to get home. I almost feel like the writers took this approach because of backlash against the moral core of Tactics Advance, though it's an opinion I probably share alone. The Ivalice games before, always offered some mature theme and deeper thinking in their characters and narratives, but TA2's main story offers little to nothing, relying on the stronger side missions which themselves are still more straightforward and fluffy than previous Matsuno Ivalice titles. I feel like this shows my feelings pretty well...
Final Fantasy X-2 - Dear X-2, please make a choice: You can either be a fun-loving tongue-in-cheek Charlie's Angel ripoff adventure starring Yuna; a somber story about politics in the aftermath of Spira's power vacuum and cultural revolution between different political factions vying to shape Spira; or it can be the tragic tale of Spira's past coming back to haunt because the dead just don't know how to stay dead in this world. No, you can't be all three. I don't mind mood whiplash but X-2 takes it to an illogical extreme with what I can only assume was three very different visions for this sequel that no one wanted to concede, and instead just had all three tales haphazardly thrown together. It might have worked if the dialogue and scenes weren't so utterly cringe-worthy that it becomes increasingly difficult to take anything remotely serious.

Final Fantasy XIII - What can I say that hasn't already been mentioned in this thread alone? Knowing me, a lot but I'll try to keep this "brief". This game has several problems. It's obvious Toriyama prefers telling gripping character stories over focusing on a plot, which wouldn't be a problem if the plot was often more interesting and worthy of exploration than his cookie-cutter characters. His character's wouldn't be so bad if A) he actually gave them the time and pacing needed to develop them properly, and B) If Toriyama wasn't a robot whose only understanding of human emotion comes from watching daytime TV soap operas.

The chapters are uneven with the first four easily being condensed down to two chapters, the Thirteen Days prologue should have been expanded into two chapters and told as a complete narrative instead of being broken up into bite size chunks that are shown hours apart from each other after they've lost their meaning, and the actual character drama parts could have been stretched out to feel more natural and build to a better climax for Hope and Sahz. Chapter 9 is when the writers suddenly remembered they needed a plot and introduce a one dimensional being who basically places the party in an unwinnable situation and then prods them with a stick for the next twenty hours before the party finally decides to take their Zoloft and fight him after he reveals he never really needed them in the first place, making the whole story pointless. The theme of the game is fighting fate, and it's obvious with the names of the music tracks but the party basically just goes along with fate and gets rewarded with a literal deus ex machina meaning the party didn't really learn anything, so what was the smurfing point? Making a deadline I suppose...

Kingdom Hearts 2 - Sorry KH fans but I still dislike this game. It starts off strong, say what you will about Roxas two hour tutorial but it had the most inventive and compelling writing in the game. Once Sora appears, the plot goes to hell. So Sora has to revisit worlds to find lightways because... reasons that are never touched on again for the rest of the series. Orgy XIII is introduced early with little setup and almost none of them get the type of characterization or screentime as their dead members did in Chain of Memories leaving most of them to feel like Mega Man bosses than actual villains. The Ansem/Xehanort plot twist is introduced with such grace that's it's taken most of the handheld side games to finally make it feel like a good idea and not a cop out plot twist to surprise fans, Goofy is supposedly killed to manipulate the players emotions but then gets retcon when we leanr less than five minutes later it didn't happen. Kairi's role in the story is so shallow she might as well had not bothered showing up. Maleficent is revived and proceeds to do jack trout for the rest of the series, let alone the game it happened in because she was just too cool to get rid of. Riku has this asinine story about turning into Ansem that has little to no logical explanation, gets resolved with no explanation and only serves as to retcon his character growth from CoM because no one bothered to buy the game since it was on the GBA. Also we can apparently just make a new Kingdom Hearts if you want instead of going through the trouble with all those Princesses and Heart of World crap, rendering everything in KH1 meaningless... Am I missing anything? Oh yeah, the cop out ending that could have segued into making Kairi into an actual character instead of a plot device if the writers hadn't decided to deus ex machina the whole deal so we can finally get a happy ending in this series.

If this was a Top Ten...

Final Fantasy X - See Raistlin's post.

FFXII: Revenant Wings - See Fynn's post

Children of Mana - Bland characters and hokey plot that serves more as an excuse plot for a pretty shallow game. Disappointed with this one.

Wild Arms 3 - Felt like the writer's were trying to top themselves from WA2's crazy plot twists. Half of the story is filled with stock characters doing their stock roles with nothing new to make them feel alive, and the other half is a bizarre story that just gets weirder and weirder as the game keeps going. While I'm always up for a new playthrough of the first two games, I really have no desire to come back to this one. It also kind of killed my interest in the franchise , though I did recently pick up WA4 to give it a chance.

Star Ocean 3: Until the End of Time - While I'm not bothered by the actual 4D Reality twist, it could have been handled better and it does create ramifications that I'm sure the writer's didn't think through until SO4 became a thing. Also the story is bit bland after it's revelation, which is odd cause you would think it's the opposite. Again, just bad execution but it's not like people play this series for the writing. What does bother me is that the characters are kind of forgettable. Cliff and Abel were interesting personalities but they didn't leave much of an impression beyond that and the rest of the characters never really interested me. One of those games where my party is mostly practical because I honestly didn't have any faves. Also killed my interest in the franchise, which is why SO4 is currently collecting dust on my shelf.