Xenogears has rather linear gameplay with a horrible random encounter rate, half-ass jumping puzzles and a very mediocre translation that at times makes delving into the otherwise fantastic plot a chore.
Vagrant Story has a pedantic, unforgiving leveling system which makes it fairly inaccessible to your average JRPG junkie.
I'm not saying that I harbor any dislike for either game but I can understand how others could.