Unneeded plot twists... the most glaring to me would be anything in the assassin's creed franchise that involves either magic or pseudo-science... It made it hard for me to get into the games at first with the weird dna memory stuff and I only got into it by forgetting about that and pretending it was only about the assassins, then magical apples made their appearance and I just lost interest completely.
Another one I didn't really like was mass effect two where at the beginning you die and are resurrected by people that you were thought were bad, join because they revived you and make a good argument but then at the end it turns out you were right to begin with and they become your enemies again, seems like lazy storytelling in a franchise that normally has really good storytelling, but I guess you can't get it right all the time.
The absolute worst plot twist I've ever seen had to be final fantasy 8... Now this was at one point in my life one of my favorite games of all time, my first playthrough was great, I was young and didn't know or care about all the ways that the game could be broken which is what most people harp on it for (that or Squall being how he is, but I was a very depressed 14 year old with a lone wolf complex and a social disorder when I first played the game so at the time I thought he was badass) and the game was great, the story made sense and fit up until a certain point, when you go to an orphanage... and find out that with the exception of one person you are all childhood friends or rivals who lived together as children and somehow all ended up back together randomly... but none of you remember it, except for one guy who is like "yeah I remember you all, but I didn't want to say anything because you didn't remember me." What the hell was that?! So then I trudged on and it picked up a little as you participate in an epic battle against the sorceress and it's good again... but then you defeat her and you realize that the sorceress was the head mistress of the orphanage that you grew up in, and that the leader of your military organization that exists to kill this sorceress is her husband... ok, so how the hell are there 3+ said military groups and how the Frick are they so relied upon already by the populous with background implying they go back much further... just how old are Cid and Edea... and your group that you thought were teenagers-young adults?, if you were some of the first "seeds" then, how did all these other instructors and people get ahead of you and where did they come from? The plot just keeps going downhill from there. The only thing I can think happened with it is that it was supposed to end on disk two with the death of Edea but the execs came to the writers and said "wait, this is way to short for a final fantasy game, lets ummm... lets just throw all the random BS you can think of in the next 10-15 minutes into the game to extend it". Thus we end up with timetraveling sorceresses possessing other sorceresses in the past in order to break time or something for some reason that isn't really explained, I mean if Ultimecia is ruler of the future why the hell does she need to rule the past where people can still stop her... it's just does not make any sense.