I don't know, long cut scenes aren't really a problem (with me) per say. Despite all the fuss, Xenosaga Episode I did not bother me like it did some. Yeah, they were lengthy but at least they were engaging in most cases. In contrast - and in response - to the complaints about the first game the second game offered next to nothing when it focused on it's gameplay which was killed by combat with horrible mechanics. The game was easily one of the biggest flops of the (that) year and easily lead to the early conclusion of the series.
I liked Xenosaga Episode I. Mostly. Elaborating, 40-minute cutscenes can feel like hours if they're poorly done (Star Ocean: The Last Hope, Eternal Sonata, Lost Odyssey to a certain extent). In contrast, Xenosaga Episode I's and especially III's just flew by.
The writing is a big contributer but I find it's the voice acting that'll make and break a game's presentation these days. And more often than not, it's very uneven.