You’re right, it’s just nerdcore backlash (I love that term!) Valkyrie Profile is also a beast quite removed from the other monsters in the genre.
You have a strict time limit measured in major “turns” and there are only so many turns you can use in each chapter to do things like search for spirits, go to dungeons or towns and towns are not used for the typical RPG things, nor are they all that focused on. Many people misunderstood this and wanted a game where you could explore as much as you like. People who actually tried to play the game the way the developers intended and not force the usual dynamics on it, found they always had more than enough turns to get everything they wanted done and in fact, usually ended up purposely wasting a few just to get a chapter over.
Another thing is that the first part of the game has an unusually long cutscene, no other part of the game is like it, so people think its going to be like Xenosaga, but it isn’t, it settles down after that, indeed, a lot wanted a more conventional story, since it comes in chunks of the stories of the dead and what happens them in Ragnarok. Again, that’s like asking that X-Com should play like Grand Theft Auto.
The last thing is the battle system, which is terribly unique and based on a mechanic that looks like it would be shallow from the beginning. But after the game lets you get bearings down, it introduces all sorts of nuances and shadows and the battle system comes its own as one the deepest there is.
So mostly reactions were of a misunderstanding of its uniqueness. Technically, there are very few flaws in VP, and there aren’t terribly important ones either, much like any other classic.
I’ve not played the port, but I did replay the game before Silmeria came out and I can say that the only thing that has aged is that the sprites get a little pixellized when the zoom functions in the battle system. That’s about it. It’s an ageless classic, especially since its mostly 2D. I’ve heard some people complain about the port, but most of it seems to be the kind of shallow, nitpicky, fanboyish criticism like one pixel is off on the second screen of the third town or “Duurrr! They changed which button does which in Mega Man Anniversary Collection! How will I live?” variety. Even if its somehow not as good as the console version, you’d have to do a lot of mangling to VP to tarnish it.
No worries, VP will forever be one of the shining lights of console RPGs and still holds its hallowed place in the pantheon of classics with aplumb.
Also ignore Moggraider. “Some” do not “claim” it’s great. It is excellent in the same way that Super Mario Bros. is unimpeachably a classic. It has been decided without consulting him, by hundreds of thousands who have had their say and is regarded by a huge majority to be that way.