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Final Fantasy. Later versions of this game (starting with the GBA version) are way too easy; they rebalanced the classes by making them all stronger (especially the weaker ones), but they failed to adjust most enemy stats to account for the party being more powerful, and the encounter rate is still high enough that you end up overleveled even if you don't go out of your way to level up.

(Final Fantasy 2 could have qualified at one point: The PSX (and, I assume, WSC) version made some questionable changes, including making spells level up more slowly; however, the GBA version fixed that issue and made spells level fast enough that you don't need to go out of your way to make magic worth using.)

Final Fantasy 3 & 4 are debatable, as the DS versions changed lots of things from their originals, some for the better (bards are now actually useful), some for the worse (FF3 status ailments were made useless).

Some prefer the NES Mario games to Super Mario All-Stars (though for a while SMAS was the only way to get the Japanese Super Mario Bros. 2 outside of Japan without importing)..

This... They gutted the game. It made me sad because I had to stop playing.

Are the new chapters compatible in eduke32 yet?

Dungeon Keeper 2

It's a bit complicated. To put it mildly.

https://www.gog.com/forum/dungeon_keeper_series/dungeon_keeper_ii_version_deiscussion
https://keeperklan.com/threads/2957-Have-GOG-DKII-which-patches-would-work-best?p=42014&viewfull=1#post42014

Hard Reset Redux - game optimized for consoles (read shittier graphics, worse lighting). I luckily have the original.
Doom 3 BFG - ruins the original's atmosphere
AvP Classic 2000 - didn't experience it but read that some things don't work in the Classic edition and they changed some voice acting and stuff
Serious Sam HD versions - unfortunately the HD re-releases had to cut/change some things due to engine limitations. My puritan nature can't get over these differences so I still play the classics.

Ragarding Metro, I have the redux versions and have also recently downloaded the originals. Planning on playing them soon. Read a lot of complaints on the Redux versions compared to the originals. At least with the first one. Again, changed voice actors, character designs, gameplay, atmosphere and lots of other stuff.

I agree. The new one contains the classic CD version, so you can choose which graphics/audio/interface you want. It's literally a matter of pressing one key.

I'm torn on this one... The "always on" torch kills a lot of atmosphere - on the other hand in most sections this really improves gameplay. I've never finished the original game (always got bored out my mind, once as late as Excavation Site).
I've actually finished BFG Edition a while ago - it simply plays more fluently.

This one is more on me and not so much on the game's update.

EF2000. I could actually play it and not get shot down nearly every mission. And then it was patched with a stronger AI. Turned into more of a hardcore flight sim, and I'm just not that good of a fighter pilot.

I wonder if %3A would work.

https://pcgamingwiki.com/wiki/S.T.A.L.K.E.R.:_Shadow_of_Chernobyl#Essential_improvements

Most games that are 3D remakes out of games that were originally made of 2D sprites.

Oooh, nice. Will have to remember that one. Frankly I only knew %20 for white spaces.

If I recall correctly, wasn't there originally LAN multiplayer that was removed to make way for the completely harmless, totally no big deal Galaxy? I am really interested in this game but want LAN option.

I can't say which version is better, but Galactic Civilization 3 is a completely different game with each patch. I have yet been able to learn it/complete a game because of it. But that's not this thread.

There's the remake of Sid Meier's Pirates!. I think I prefer the 80s version because it doesn't have that dancing rhythm game... But then the remake's ground battles are better. So it's a wash.

Railroad Tycoon 2, I prefer over Railroad Tycoon 3. The transition to full 3d didn't work well. And then when SM's Railroads came around, it was bad.

Sims 3 is better than Sims 4 by almost all reports. Not that I've played 4 due to DRM.

Deus Ex definitely beats Deus Ex 2 in every meaningful way.

Now trying to think of games where patches/updates of the same game ruined the experience, hmm.... Armello was ruined by their move to DRM + microtransactions. I'm sure some strategy, probably RTS, at some point irked me with a balance change.

OH! Here's one! Diablo 2 got worse when they added in "synergy bonuses". It pushed you into direct builds rather than letting you have more varied options. Around the same time those were added (around the same time as the Lord of Destruction expansion pack), they broke the sorcerer asymmetry. Before that, the three "masteries" for sorcerer were completely unique: Cold Mastery reduced enemy resistance; Fire Mastery increased damage; Lightning Mastery reduced the mana cost for its related skills (which worked really well with Lightning having wide ranges for damage so you'd repeat cast it more). After those changes, Lightning Mastery became also plain "increase damage".