Like I said, if the the direct consequence of a choice happening off-screen in the sequel retroactively renders the entirely trilogy irrelevant to you, that sounds like your problem.
Sure, but you do know why people have these problems.
The trilogy set up the expectation of continuity, over 5 years of games, novels, comics and whatnot. The expectation of the next installment.
In the end, its conclusion wasn't nearly good enough to alleviate that. It kind of made a good chunk of the experience a bit irrelevant.
Hence, if it's left in that state, that feeling remains.
Plus, people feel there's still a lot of life in the setting and they don't want it thrown away.