Reading some of these - I think BioShock.

The original was heralded as a game that saved and refreshed single-player FPS games. It was one of the most critically acclaimed games of all time.

The pressure of living up to the original may have created development issues and sky-high costs with Infinite. I thought it was a fantastic game that stood on its own. But at the end of the day, it didn't perform well enough to keep Irrational Games alive.

Metal Gear Solid. I don't think the rest of the MGS games are bad , far from it-- it's just... There's something great and special about the first one and this is not present in the other games. I don't know how to explain exactly, but... I think it's the atmosphere, music and the overall aesthetics of the game. I know it sounds weird but seeing the low poly characters with the weird PS1 warp textures is great, and... I think it really adds to the atmosphere of the game? The soundtrack is really different from the other games too, probably because they changed the composers. So... yeah. Metal Gear Solid.

Symphonia is my favorite as well,  but Vesperia came very, very close. They also nailed the presentation. Graces was when they started using paths between major areas instead of a proper world map. I've liked most of the games since then, but I really want to either see another Vesperia or see Arise have a drawn-to-scale world map along the lines of the last two console Dragon Quest games. 

I never played CoM, but I definitely was not impressed with either Legend or Dawn of Mana. I did enjoy Sword of Mana, the remake of FFA, because it was redone in the style of Trials, though I definitely wouldn't say it's as good as Trials.

Xenosaga was not only a huge step down from Xenogears, but the series itself went steadily downhill from the first episode. Xenoblade Chronicles more than redeemed the Xeno meta series, however.

I generally agree with this opinion, but with the added comment that for me Berseria is a return to form. I like it as much as I liked Vesperia back then. All games in between them feel like a complete downgrade. 

Indeed. The first two games were fantastic, and it was a gradual decline after that until Angel of Darkness became the nadir of the entire series. I do like the Crystal Dynamics trilogy though.

Tony Hawk's Pro Skater 2 is easily the best of the franchise, and everything since has failed to live up to that benchmark. There were refinements and experiments in future titles, but nothing was ever as fun as this one.

I kinda agree with you. Especially since the story was so well executed, the bosses were so epic, and the characters were so memorable BUT for years I swore Metal Gear Solid 3 was the greatest game of all time. It still might be but I haven't played it in a while. I could see a lot of people saying MGS1, though. It set an incredibly high standard that even its own remake couldn't overcome.

I would rather pick the ones that Bioshock tries to imitate, namely System Shock 1+2

I was joking about CoM, it's not that great. I thought it was ok, but I haven't felt the need to replay it since it released. It wasn't a return to form, that's for sure.

Paper Mario: The Thousand-Year Door, maybe. There hasn't been another game like it in terms of gameplay afterward in the Paper Mario series. The fact that it was so amazing makes Paper Mario's changes all the more sad.