I think the gameplay really is a major part of it - it definitely shares a lot of similiarities with Xenoblade, but it plays much more drily and has an even greater focus on automation than that series, which doesn't exactly have the greatest mass market appeal, I assume.
Another part would be the story - it doesn't really feature much inter-personal drama or character development for the cast (aside from Ashe and a couple scenes for the rest here and there) and is more concerned with the grand picture and political scheming between side characters.
(Again, my favourite part during the my second go-around. Especially since the game trusts the player to understand what's going on in the plot without spelling every little detail out over and over again.)
There's a reason Fran takes up most of the few callbacks to that game that tend to pop up online - she's the only thing approaching the kind of waifu character that people usually latch on to in the game.
Hell, even the ancient magical artifacts are framed more like WMDs in that game than the usual creeping influence of malign gods bent on world destruction. It doesn't present the way JRPGs usually present.
With all that said, the game is also just plain flawed - the pacing is godawful for example.
(Whoa, sorry about the wall of text - I need to teach myself how to be concise again...)
Nono, that was very infornative and fun to read