Currently playing Blood Waves. Very flawed and buggy game but slaughtering waves upon waves of zombies is very satisfying.

Love building death machines where they meet their doom.

I guess Cities: Skylines is worth mentioning, both the first and the second game. The second game obviously has more notable issues, but honestly, I haven't looked back since the game released. It improves in some key areas for someone who played the first game with only relatively few mods. As for the first game, traffic was both the really interesting and fun part as well as the annoying part due to the terrible traffic AI, and otherwise the game was just way, way too easy. Still, the flaws don't really get rubbed into your face, so living with them is generally easy enough. But when the second game was finally released, I was so done with all the traffic issues and the duct tape holding the game together with all the mods all their own designs that didn't really match the vanilla game. I'm sure the flaws of the second game will also start to annoy me more at some point, but I'm hoping the game gets improved enough before that happens (and I'm quite confident that's the case).

Indigo Prophecy or how it’s known in my country Fahrenheit, such an unforgettable game for me but there are some major plotholes! Lol

Target Earth/Assault Suit Leynos

Early Genesis run-gun game. Masaya is one of my favorite 16-bit-era developers. Langrisser. Assault Suits games. Hellfire. Gynoug. Cho Aniki. Gleylancer and more. It's nowhere near as polished as a Contra or Gunstar Heroes. It was a bit stiff and punishingly difficult but there is something lovely about it, from the stellar OST to some cool secrets. Finish the first level by only killing the boss and no other enemies? Unlock every weapon in the game.  For every level, you choose a loadout.  Future games were polished great games like Cybernator/Assault Suits Valken or Assault Suits Leynos 2. The first game is my favorite and it even got a great remake on PS4/Steam. It's often on sale for a couple of bucks if you like a good run-and-gun. The remake is better than the original.

Ridge Racer Type 4 (PS1) has a horribly grind system for collecting all cars, which relates to how you basically have only one game mode where you always play the same 8 tracks with 7 opponents, starting last. Repeat 200 times (getting every possible result with every available vehicle) to get the cool Pacman car.
But it was also one of the most enjoyable driving games of the many I've played.

There would be many games I played once, enjoyed for some reason, but hated certain parts.
Mafia 1 (original) had much great, but FPS parts were awful.
Nocturne is a nicely atmospheric horror game with terrible gameplay.
Betrayal in Antara is more a nostalgia piece for me, but it had its moments. (And I don't mind the graphics, even it was said to be ugly and aged already when it came out.)

Wing Commander: Privateer I've played number of times and that really among games I love. But the fully linear story - where it's game over if you ever fail a story mission - is a big flaw (even if that's how it often goes with generally "open world" games).

For me:

Mass Effect

The framerate's all over the place and the cover and melee systems are awkward, but the universe Bioware created is just so deep, so rich, and so compelling to engage with that its technical foibles do little to dim its brilliance.

Epic Mickey

It's such a charming and likeable throwback to the golden age of 3D platformers that the sometimes janky camera and framerate hardly bothered me.

Bayonetta 3

The graphics are poor by Switch standards, but the gameplay is still incredibly fun, and its highlights are great enough to outweigh its shortcomings.

Banjo Tooie.

Despite the flaws in level design, pacing and some broken mechanics/missions, I just love replaying whenever I get a chance.

Love the atmosphere, the lore, the worlds, characters, the conversations, bosses, the abilities/transformations, puzzles and the mini-games. Way better than Banjo Kazooie, the first one I can't hardly say I enjoyed 

The original Nier came to mind first. A great story and wonderfully written characters with one of the best soundtracks of the generation, but you can definitely see the limits of the budget in the game's graphics and gameplay, and it has some issues with stretching the game's length unnecessarily.

Elemental: War of Magic and it's replacement Elemental: Fallen Enchantress.

Both were deeply flawed, so much so that Stardock gave every buyer of Elemental Fallen Enchantress for free. But that one also was pretty rough around the edges, so Fallen Enchantress: Legendary Heroes got released. Nominally an expansion, Legendary Heroes includes the entire Fallen Enchantress content plus all the additions it itself brought to the game, and has fully replaced Fallen Enchantress in their storefront, just like Fallen Enchantress fully replaced Elemental at it's release.

Eador: Masters of the Broken World and it's expansion, Eador: Imperium.

As broken as in the title, with a very pesky memory bug (which will overflow even if you 1TB RAM), so save often! Also extreeeeeeemely long and slow (The story is divided into several "rounds" where the main protagonists fight over the shards of Eador. On bigger shards those Rounds can easily take longer than a full Civ campaign. Did I mention that you have up to 60 such rounds before the story is done?)  and very difficult (there's a reason why the "easy" setting blurb is "A Reasonable Choice"), but I just love it.

Heroes of Might & Magic IV.

Most people prefer the third one and dislike the fourth due to the changes it brought, especially on the units and city developments. However, I actually prefer this one over the third entry due to the other changes it brought (caravans sending troops from one place to another; flaggable buildings that produce units or random ressources, etc...) and the better campaigns. 

Might & Magic VIII.

Might & Magic VIII was the last title of the Erathia trilogy, and certainly the most rough around the edges: The world looks quite a bit smaller than the first two titles and monster variety is down. But those all pale to the balancing: Minotaurs and Vampires are wimps, while Dark Elves and especially Dragons are absolutely broken. Minotaurs, Vampires, Dragons? Yeah, those are some of the possible party member classes in this game, which is very cool. But trying to balance their traits with their mythological skills broke them into either useless or absolutely OP with little in between (well, the Troll class is pretty balanced and refreshing - but that's sadly the only one). Plus, at some points in the game the game forces some party members on you, and by the second time this happens you probably already have your dream team assembled, forcing you to let go of one of them for the new guy.

But other than those goofs and quirks, it's a great RPG, and they even fixed some bugs that were present in VII (which runs on the exact same engine).

Yep, the runey system was godawful. I tried to avoid doing anything with those as much as possible

Also, the fast that tools did more damage than weapons. I went through entire dungeons armed  with a watering can and a fishing rod as backup when the can was empty...

Yeah Banjo Tooie is one of my favourite games of that generation; the framerate is poor, but the rest of the package is so strong that I had a great time anyway, especially the bosses, soundtracks, humour and variety.

Same for Conker's Bad Fur Day the following year, terrific game in spite of its performance problems.