Xenosaga Episode 1 has only been out a little over a week, and already there is speculation over the next episode. What follows is basically spoiler free.
Based on events in Episode 1, it can be assumed that Jin Uzuki (the character that looks very similar to Citan), Shion's brother, will play a major role in Episode 2. This also means that Xenosaga Episode 2 will be a mostly single player game; how the previously announced online capabilities for the sequel will be meshed is anyone's guess.
Xenosaga also directly states that Zohar will be central in all six episodes.
Look for RPGFan's review of the import of Xenosaga soon! Xenosaga was released February 28th in Japan; no US release date has been announced yet, but look for news in the next month or two as E3 approaches.