Thank you Hobbs! That's exactly what I was thinking about where the narrative is changed, I'm just not sure that about actual gameplay features being changed, I'm still kinda stumped on that one. Any others? I had thought of the censoring of the panties from the remake of Double Dragon, but that's not quite the same thing again.
This sort of thing is rife in MMOs and competitive games. Game "balance" for WoW or LoL probably creates more drama than the rest of the topics related to those games combined, even microtransactions. SWTOR didn't ship with homosexual relationships between the player character and NPCs, spawning considerable weeping and gnashing of teeth, so one of the first new planets included such romance subplots (albeit skimpy ones that weren't very good and didn't do a good job of fobbing off complainers). That sort of thing.
But here's another
Mass Effect example:
In the first game, gunplay centered around weapons that could be fired automatically until one's heat sinks reached capacity, at which point the gun would be unusable until heat was discharged. One could delay reaching maximum heat by firing in bursts. This system sounded innovative on the face of things, but in practice turned combat into something slow and clunky with minimal amounts of movement and finesse. Spray and pray, run around aimlessly, and don't worry about running out of ammo because you just have to wait until the heat buildup dissipates. Certain builds could even fire endlessly with no heat buildup, especially if certain mods were employed. No explanation for this obvious violation of the laws of thermodynamics was forthcoming.
Intelligently, the design team abandoned this system for
Mass Effect 2, switching to a "thermal clip"-based set of weapons. There was a lore explanation for this, but it functionally meant that weapons once again relied on ammo, reloading, and finding ammo pickups throughout the levels. Although this was met with general approval from people with more than three brain cells who understood anything about gameplay and lore, there was a hard core of dissenters who protested against this decision, for the following bizarre reasons:
1. They didn't like the "feel". Infinite ammo and heat discharge seemed more futuristic.
2. Ammo reminded them of
Call of Duty games, which are
prima facie bad or something.
3. They thought the lore explanation of the thermal clips was lacking, although apparently the lore explanation of endlessly firing weapons was perfectly fine.
There was also these reason, which mostly went unstated but implied:
4. They sucked at playing the game and kept running out of
thermal clips ammo.
5. They were overcome with lolstalgia and found themselves incapable of recognizing the first game's many, many flaws.
1
These people mostly would've been obnoxious irrelevant idiots who just needed to L2P if not for the makeup of online gaming forums and the Internet silent majority syndrome. So for several months after release of ME2, when the game was receiving virtually universal praise from every major media outlet and reviewer, BioWare's message boards were swarming with threads complaining about thermal clips.
To their great credit, BioWare's devs elected not to mess with the second game's mostly-excellent gameplay as they were designing the third game. Thermal clips stayed in, along with the way powers worked and pretty much everything good about the ME2 UI. However, this did not mean that a bone could not be thrown to the thermal-clip whiners. Two separate assault rifles made appearances in
Mass Effect 3, both in downloadable-content missions, and neither of these two, unlike the vast majority of the weapons in the game, used thermal clips. Instead, they both relied on the old overheat mechanism from the first game. BioWare included the old system after all, purely on request.
Amusingly, neither the Prothean Particle Rifle nor the M7 Lancer assault rifle gained much currency in ME3's new multiplayer mode. Neither weapon required DLC to access in multiplayer, so anyone could get it if she got lucky with her mission reward packs. But when stacked up against the thermal-clip weapons in a setting where efficiency
really mattered, the overheat-based ones fell short. Which is exactly what BioWare and a few intrepid

mischief

forum warriors had been telling the unwashed anti-thermal-clip masses for years, but whatever.
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A more minor example is how planet scanning was deemphasized from
Mass Effect 2 to
Mass Effect 3. The planet scanning minigame in ME2 was in no way necessary; it was a way to get resources to acquire upgrades for your weapons and armor. You could skip it quite easily and still beat the game on the highest difficulty level with any story results that you wanted.
Nevertheless, some people felt compelled to scan ALL THE THINGS and then had the temerity to complain about how they were "forced" to waste their time collecting vast stockpiles of resources for which they had no actual use. In effect, these lunatics were blaming BioWare because
they wanted to be completionists (and completionists to a ridiculous degree, since they were scanning
just to say they had scanned out all the resources, not confining their efforts to only those resources that they actually needed for upgrades) but also wanted completionism to be easy. Idiots.
In this case, however, BioWare did fully acquiesce to requests.
Mass Effect 3's planet scanning was stripped down almost completely. There were no resources for upgrades; instead, planet scanning was based on objectives for missions with a pointer included to make each scan quick and painless. Ten seconds tops. A victory for the little guy.
Of course, the joke was on them (us?), because the thing that
replaced planet scanning was arguably worse. The new scan minigame took place on the galaxy map and pitted the player against the Reapers; too many scans and a few dreadnoughts would be on your tail, with auto-death the price of failing to flee the system quickly enough. It also became drastically more difficult to actually locate the things you were trying to scan. Nice job breaking it, whiners.
1 - In my experience, BioWare's customers are the absolute worst about this. You'll have people moaning about how previous games were the best with any franchise, but for whatever reason, the people who think that the best Mass Effect game was the first one (and the best KotOR game, and the best Dragon Age game, etc.) seem to have a disproportionate presence in online fora. You won't find many people claiming that about the first CoD game, or the first GTA game, or the first WarCraft game, or whatever. I am at a loss to explain the phenomenon.