Chrono Cross and Apollo Justice are both the first things that come to my mind, and I'm surprised only one other person has mentioned them. Whatever you think of them on their own merits, they kind of suck the enjoyment right out of their predecessors. I just choose to believe both of those games are, like, what-if stories, or fan fiction.
In particular, Apollo Justice is a self-insertion fan fic where the writer realized part way through that they couldn't think of anything interesting to happen to their character, so they dragged Wright back on to center stage after unceremoniously booting him off.
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Ace Detective in Sir Chris' Police
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