Most definitely this; Star Ocean, Suikoden, Final Fantasy, Valkyrie Profile etc. were never quite the same on the PS2. I still loved the genre, but those PS1 JRPG's were something special. As for Valkyrie Profile, I loved the battle system in Silmeria, preferring it to the first game. However, VP2 didn't really come that close to matching the atmosphere, soundtrack and visuals and story in VP1.
You'll probably have a similar experience with Xenosaga. It won't live up to the ambition and scale of Xenogears, but they're pretty good games. XSIII holds up incredibly well and is the true gem of the series. It's such a shame it took them three games to get it right. By that time, the series was dead in the water.