I kinda remember Shion drastic personality change from 1 to 2 is what most people complained about.
I think I read it back then cuz they have different producer/writer, shit just goes wrong big time in terms of character personality and story direction. To the point one myth says the game artist release a fanbook/doujin, and have one whole page ranting about the guy who is in charge of 2 screwing Xenosaga.
There's prob more stuff on what goes wrong behind the scenes, if you look at Xenosaga related fanpages nowadays or something. 2nd game is pretty much where everything falls down and never recover. Monolith just end it at 3 afterwards (as opposed to planned 6).
And obligatory, as per Harada (Bamco), "Xenosaga doesn't make money, so no remaster for you guyz".
That would be an interesting read. But I think the reason why it wasn't 6 meandering games is the same reason there's no remaster, the series just doesn't make money. ---