I believe The Beatles: Rock Band came the closest to being perfect. Eveything about that game was just beautifully done and the only things missing was Pro Drums, an option for Keys, and a few more Beatle songs (Hey Jude, Strawberry Fields Forever, Yesterday etc. etc.)
Not OP, but a personal example is Halo: CE and Halo 2 vs. Halo 3.
Halo 3 is one of the most polished video games of all time, period. It is insane how much work went into it, and how professionally made and “complete” it seems. The only complaint I could make about it is that it’s narrative fell horribly flat after Halo 2 being a masterclass in saying a great deal by saying very little.
For the same reason I also find it slightly boring. I grew up with H3, I love it, I still play it a lot, but it’s gameplay is boring.
Now, Halo: CE on the other hand… It’s full of “exploits” that make it infinitely more interesting long-term, and seemingly by sheer luck, all of those unintended mechanics feel like they balance out into something like coherent. Stuff not mentioned in that video includes how every weapon had different melee speeds, melee damage was affected by your current velocity, and odd weapon uses like the AR’s wall of bullets being perfect for searching for camo players and the plasma rifle being good for flanking because it’s hard to turn around if you’re getting shot with it. Combat Evolved is weird and that makes it fun.
Halo 2 is the same to a lesser extent with it’s own button combos, but the mechanical polish was starting to creep in and the button combos it did have were both game-breaking and necessary to play “well”. You could literally double the fire rate of the most important gun in the game, but you needed to give yourself RSI to do it. The Smash Bros. Melee of Halo.
What about TES 4: Oblivion? People trash on Bethesda so much these days because their games are kind of janky and to some people, just not very good, but oh my god Oblivion’s got the special sauce even if I sympathize with people hating it. There’s a reason it’s soundtrack is constantly used as a backdrop for odd conversations now. It’s “problems” added up to a bizarre, “cough syrup trip” tone that worked in it’s favor by the time The Shivering Isles came around. Everything about it feels wrong and it’s oh so right.
S.T.A.L.K.E.R.? Not the Open X-Ray freeplay mods everyone plays these days, but the honest-to-god original Stalker series that people mostly forgot about or only claims to have played. There’s so much weird stuff going on in Stalker. Glitches? Oh, the Zone is just acting up again, it does a lot of weird shit, learn to deal. Call of Chernobyl did some really strange stuff with it’s gunplay. You can’t be truly accurate without “stabilizing” yourself by sitting totally still for a moment, but the game never tells you that. The locational health system is so extreme that people’s arms and legs might as well be bulletproof, or maybe they’re just black holes for bullets. The first guns you get pack astoundingly poor accuracy on top of those problems. The end-result is that you get… weirdly believable firefights sometimes, where people are actually laying down covering fire and flanking around to actually land a shot. But sometimes you’re better off just going sicko mode and sprinting up to a crowd with a live grenade, because you’re in too bad of a position to behave sensibly.
And, of course, IcepickLodge’s games are just the cream of the painfully sharp edge crop. Why does this game suck? Because plagues suck. Even though IPL themselves have been disappointed twice now by how Pathologic turned out, that’s still a very true statement and Pathologic is still rad as hell.