Well, I'll ignore the obvious ones mentioned already (DMC2/Xenosaga Episode II) and go with a few FF ones. The main two are Crisis Core and Revenant Wings.

Crisis Core has a plot that feels like uninspired fan-fiction that basically copies and pastes the main Shin-Ra shenanigans of FFVII and introduces my vote for the worst villain in the series. Genesis doesn't even feel like a villain, just a poorly written-in cast off who the game spends a majority of its time trying to pass them off as cool and sympathetic and instead he comes off pretentious, bland, and genuinely unbelievable unless you like Gackt's looks (well he is pretty). Made worse by them tampering with some of the most iconic moments in the VII mythos just so they can post a picture of him there to tell the fans "he was there! so he's like totally a part of the VII mythos!" but instead it pretty much destroyed my faith in the companies abilites to handle their own IPs...

Combo this with a bland action game combat system (seriously, you guys just made KHII and you gave me something that makes KHI's battle system and camera seem like the epitome of action games) combined with a Normal Mode that has the bare requirements of needing to breath in order to beat it. Mission Modes that are horribly repetitive and lose their luster after you finish the first hundred of the 300 samey missions. The story mode actually utilizes a few simple but fun mini-games, the mission modes ignore them and stick to "explore the small dungeon, fight the nearly impossible to avoid 'random' encounters and find the treasure chest" formula. Hard Mode might as well be renamed "Zack must die mode" cause the only way to get through hard mode is to complete almost everything in Normal mode. They jacked up the stats of all the monsters and bosses to the point where you need the Break HP limit Gear and fully HP+++ effects on your materia to survive a blow, now the broken dodge roll move still allows you to dodge most of the things enemies throw at you but this is SE so we have to do something cinematic so every boss creature has an unblockable/non-dodge-able cinematic attack that will basically make trying to dodge roll your way through hard mode impossible so your back to playing mundane and tedious Normal Mode...

Last Order looked awesome and gave me some high hopes for Crisis Core, bad gameplay and an even worse storyline that in my eyes spits on the good name of the original just makes this one of the worst titles to come out of SE this past decade (I have yet to touch DoC though...)

FFXII:RW is probably the second worst title out of SE in the last decade. I don't even play RTS games much and I can tell its pretty bad. Still, I know SE doesn't do this kind of thing so I've been pretty lax about it. Yet even with that, its hard to ignore how one-sided and terrible some of the mechanics are being used.

Example:I tried to fight a boss character in an epic battle but because she gets the ability to randomly spawn minions at her beck and leisure and she is horribly overpowered (the Espers and Summons are jokes compared to her) made the battle frustrating to beat, until I threw all my resources into building and unlimited army of flying enemies (her weakness) and sent them her way while my party sat back on the opposite side of the screen next to a summoning circle to keep the minions coming. Her minions usually ignore my units to attack my character leaders and we are more than capable of dealing with them when I don't have the bloody winged angel of death backing them up so I literally cleared the mission in about ten minutes, what bothers me is that you can do this strategy in almost every boss mission and the other missions are not nearly as tough, not to mention it doesn't take much to "grind your way to victory" for some of the medium level missions. It just seems like SE was not talking to the right people when they decided to get their crash course in RTS design.

Beyond bad game mechanics though, the plot and characterization of the characters are awful. Everyone feels like some weird caricature of their former selves with many of my fave characters joining your party and then becoming bland mutes in the background of the story. The introduction of Filo and Kytes as major characters is also exasperating as they are both annoying and are obviously inept to adventuring but your party keeps them anyway (to be fair, Kytes is a great unit but god is he annoying) and characters like Ashe and Basch get one token scene and then drift into the background like they were NPCs. I know unlockable hidden characters that got more screen time than these two. Even Balthier who is a major factor of the plot for the first half while he strings along Vaan and company only to finally join the party and drop out of the plot to become another supporting role. I won't even get started on B'Gamman

Not to mention the plot has too many similarities to previous efforts by its director/writer. (SPOILER)The Yarhi are mysthical spirits that can effect the real world and are imprisoned by an evil force (worshiped in the real world as a god and is the sacred religion the Aegyl follow without question) that prevents them from staying in their own world so they use an incarnation of a dead person to tell the real world what going on and to free them... Am I the only person who doesn't feel this sounds a little too close to the basic premise of FFX? Not to mention the pseudo main villain has a few similarities to Shuyin from X-2. There is is some original stuff but a alot of the plot feels like rehashed work and its obvious its director and writer never bothered to try and get a real feel for XII's characters or stay within some form of canon.

RW is proof you shouldn't hand creative control over a sequel to people who were not even involved with the original IP, CC is proof you shouldn't bother waiting to make sequels to crap 10 years after the fact when your mental framework has changed so much. You can't just pretend you can approach the story the same way you did years ago nor should you feel just because you did write it then means your aged writing style is appropriate for it now. Seriously SE, stop making sequels with FF in the title.