The third one took the best from the first two battle systems and got rid a lot of the bad. The break thing in two was pretty horrible near the end game. You had to charge up your boosts so you could chain two characters together to get the right break sequence, and then hope for the best. Some of the battles near the final boss took an obscene amount of time, unless I was just screwing up a lot.
I liked the battle system in the first Xenosaga though, because you could customize and abuse it more. I remember checking a guide when I got to a boss I thought was just an easy kill that lulls you in before a bigger boss. Turned out the guide said he was one of the toughest in the game, and I was walking all over him. The trick for me was to assign a "hit all" skill to one of the easy button combos, and then just harvest skill points in that forest with the goblins, or whatever they were, that rushed you at least six at a time. Late game, I was using my characters for the AGWS battles because they were faster, and could hit harder.
As for disc 2 of Xenogears, I remember when I re-played it once I was a little older the thought hit me that maybe they were running out of money or production time, so they condensed it to a big run on cutscene with boss fights, and two and a half dungeons thrown in because they had the foresight to create them early in the development cycle. I still really enjoyed the game, it just felt rushed at the end.
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Xenosaga/Xenogears Appreciation Thread