I know it's over a year later, but I thought I'd give this thread a little love.

I think what you're saying is probably true for the Phantasy Star Online era. I haven't played those ones much (I'm into the classic series, not so much Online) but I got a bit of a vibe that the story was just there to give context to the gameplay, not something you appreciate in its own right.

As for the classic series (I, II, III, IV), I think it doesn't have to be a binary "you either play for the story or for the gameplay". I think the stories for the classic games are quite good (and much better than some RPGs which are meant to be played for the story!) but I think Sega never forgot that they were making games. They're not like Squaresoft, who focussed on narrative and presentation at the expense of the games being fun. (In my opinion, of course.)
The first one is a good story for the time, and while it's not exactly fine literature, it still has charm today.
I think the second one has an excellent story, and I think most people who talk about Phantasy Star single out that one as having a great story. (It has to, because all the grinding, and those confusing dungeons, have made the gameplay age badly, lol.)
The third one... Well, everyone knows it as the black sheep of the series, and in my opinion, that's accurate. Its story was ambitious, but doesn't come together like it should.
I think the fourth one's story isn't as good as Phantasy Star II's story, but it's still pretty enjoyable as an RPG plot. It complements the gameplay well, so you have fun playing it, but also feel like you're achieving something bigger. It also gives a nice conclusion to the story and world from the other games.

Well, that's my defence of the stories of the classic games. I hope this is the kind of response you had in mind when you posted!