But as far as making a list like this goes, I do think an initially buggy game is going to be at somewhat of a disadvantage. It'll lose a few people who might have put it on their list because they had a bad initial experience with it. Being later told "oh there's a patch" isn't really good enough.
(Also I think lists like this inherently bias towards earlier games in a given series, more nostalgia and all that, for all that that is something I pretty much share Cid's disdain for.)
I picked up on a couple apparent biases, none of which especially surprised me:
1) A general bias towards earlier games in a given series when those game were at least passable relative to their era of release (e.g. WA1)
2) For series which span multiple console generations, a general (if somewhat weak) bias towards the first game in that series of a given console generation (e.g. FF7)
3) A general bias towards specific games which came very late in a given console's lifecycle, as well (e.g. Persona 4)
4) A general, fairly strong bias towards specific "generic JRPG" titles on consoles that had very few such games that were not ports released for them (e.g. Golden Sun games on the GBA, Bravely Default on 3DS, Skies of Arcadia and Tales of Symphonia on Dreamcast/Gamecube both, Phantasy Star 4 on Genesis, Tales of Vesperia on Xbox 360, etc.)
I've long held a general impression that among the internet at large, most JRPG fans seem to value execution over innovation to a degree; that is, they'd rather have moderately well executed but unambitious/stale gameplay (like Suikoden 1/2 or WA1 or Earthbound) over either something more experimental that ended up having significant flaws in execution (like Suikoden 3 or FF8) or something that massively changed the character of the gameplay from what series fans had become accustomed to (notably Wild Arms 4). There is, for example, a reasonably large (or at least vocal) subset of the WA fanbase of which I'm aware that hated WA4 for doing away with the style of dungeon puzzles found in WA1-3 and ACF. (As you'd guess, most of them are also rabid Lufia 2 fans.)
The market during the SNES and PS1 era would seem to bear this trend out for at least that period of time; consider the large number of games from that era which have conventional, unambitious turn-based menu combat in the Dragon Quest mold, even if they aren't explicitly DQ clones (like, say, Earthbound undoubtedly is), and consider that most of these games are extremely popular. However, if the PS2 and later eras are any indication, the fanbases for such games, while vocal, aren't enough to fund development costs for such games on modern consoles without some other factor to draw appeal from outside of that niche, as evidenced by how few of these kinds of games appeared on later platforms relatively, combined with the growing strong bias against launching new RPG IP on home consoles due to rising development costs. Case in point: the only JRPG franchise I can think of that started in the 6th generation (PS2/GC/Xbox) and has continued beyond it is Disgaea, and the only JRPG franchises I can think of that started in the 7th generation (PS3/Wii/360) and have continued beyond are Hyperdimension Neptunia and Xenoblade (I consider the latter fundamentally distinct enough from previous Xeno- titles to be effectively its own entity). (If you can think of others, by all means, please fill me in.) Disgaea somewhat heavily relies on appeal to a very specific demographic (enjoyment of grinding in a game-breaking fashion) while Neptunia very heavily relies on appealing to the moe anime otaku demographic, and neither they nor Xenoblade have anything really like what I'd consider "traditional JRPG" gameplay (the only games with such gameplay in recent memory that have been localized are pretty much Bravely Default and Final Fantasy Dimensions).
General observations, amusements, or things on the list I found surprising:
1) I was happy to see Persona 4 top Persona 3, as in many circles on the internet people tend to really overhype Persona 3 for being edgier.
2) For the reasons described above, the placement of S1 and S2 doesn't surprise me much. S1 and S2 are both unambitious generic JRPGs in gameplay, and fairly well executed at it (obviously S2 is more polished in this regard, and appropriately ranks higher). S3 had the weird pair mechanic and possibility of friendly fire which I know I'm not the only person who didn't like it, S4 doesn't really need to be explained, and it's reasonable to assume that many casual fans of the series who played and liked S1 and S2 and didn't like S3 or S4 may simply have just never given S5 a chance.
3) Likewise with Wild Arms. WA1 undoubtedly gets a large boost from being the first competent RPG on the PS1 to be localized, and is similarly an unambitious generic JRPG in gameplay with the addition of dungeon puzzles (pulling in the Lufia 2 demographic). While WA2, WA3 and WA:ACF retained the dungeon puzzles, they took some fairly large steps away from generic by mixing up the world map mechanics; it's probably a safe bet that at least some casual fans of WA1 saw this in WA2, didn't like it, and didn't try any further entries in the series.
4) Skies of Arcadia's placement is probably attributable to it being the only traditional menu-based JRPG on the GameCube (and being one of the only such RPGs on the Dreamcast, as well, but I suspect the GameCube has a lot more to do with it). Tales of Symphonia also strongly benefits from this despite being an ARPG.
5) Likewise for Golden Sun 1 and 2.
6) I am very surprised Barkley had that much acclaim - not because of its quality, but because of its sheer relative obscurity.\
7) Witcher 3 probably is subject to a healthy dose of new release skew.
