Becaue I feel like it, a couple issues I have with Final Fantasy 6/9:
* During attack animations, time doesn't stop, but new attacks can't be made. This leads to the action queue getting backed up, which makes it take a while between entering a command and actually executing it. It's bad enough that I have found myself (with battle mode set to Wait) opening a submenu and simply waiting for the queue to empty; I shouldn't have to do this. It gets even more ridiculous when a strategy is to use attacks with long animations (like 9's summons) to give certain effects a chance to expire, or in FF9's case, for Auto-Regen to fully restore your party, which just seems silly. (Note that FF6 regen doesn't heal you during animations, but it can queue up a heal to occur as soon as the animation finishes.)
* The way stat bonuses at level up work. Basically, to boost your stats, you need to have certain things equipped at the time of level up; this makes it overly necessary to pay attention to the precise amount of XP needed to level. It also encourages intentional XP avoidance, which means you need to avoid much of the gameplay if you want to optimize your characters. It's, in particular, a case of the issue I call (and have seen called) "missable stats"; unless you play through a large portion of the game without leveling up, your stats won't be as good in the long run. I actually think these games would be better if stats did not increase at level up at all.

(Yes, these issues apply to both games, and not the two in-between. FF8 solves the missable stats problem by providing a couple other ways to permanently boost stats (seed-like items and an ability from the final Guarding Force), though of course the game has other flaws.)

To me it quite often is related to the user-interface, ie. does the game have things that make playing it feel nowadays quite cumbersome, something that you normally wouldn't just want to put up with anymore. Doom has this too, without mods.

For instance, Dune 2 and Warcraft 1 haven't aged that well either because they are quite cumbersome to play, like in Dune 2 having to give orders to units one by one (in real time), and in Warcraft, while you can draw-select several units, you can't save (memorize) the unit groups e.g. in the number buttons, something that is taken for granted ever since Starcraft and Total Annihilation in RTS games. Maybe Warcraft 2 also had that too, I don't recall for sure. Starcraft and Total Annihilation, on the other hand, have aged quite well for RTS games, in my opinion. Sure you can only have like 8 units in a group in Starcraft, but the gameplay is optimized with that in mind, ie. you rarely need bigger groups anyway. It is not a game where the screen is filled with hundreds of units, more like a few dozen at most.

The original System Shock also hasn't aged that well due to the clumsy user-interface (moving around and fighting), but luckily there are the mods adding proper WASD+mouse controls to the game, making it great again. On the other hand, Magic Carpet has aged extremely well in my opinion. Besides graphics, I can't think of much I would change in the game, in order to "modernize" it. It is 100% joy to play, even today.

There may be some other things also that haven't aged that well in games, including graphics (if they are so low res that they really get into the way; I'd say Falcon 3.0 is like this, maybe also Red Baron), physics of the game (especially with racing and flight simulation games), and sometimes even the audio/music (e.g. I just can't bare PC games from the 80s much due to the PC beefer sounds, and frankly most Adlib-sound card PC games annoy me as well, as I grew and got accustomed to superior Roland MT-32 music in PC games).

Oh and cheesy FMV in some 90s games seems so out of place nowadays (and in many cases already back then), like in Terra Nova etc. Luckily Terra Nova gameplay is still quite good so you can just skip the cheesy FMV parts with B-grade actors.

That has nothing to do with its age by the way, it was a deliberate design decision (a really great one).

Metal Knights 95

Several years ago I was playing in loop on the demo version, I was having fun collecting all the gold mines and cities for fun, but inevitably as I was playing solo and that demo didn't provide any AI I was bored quickly.

I thought that the game was quite nice, there is a good atmosphere and the fights are pleasant (at least in the demo).

In short, later I was able to buy the Gold version which includes I.A., and the drama: the turn of the AI is completely masked, so if it attacks us, the player does not see the tactical fights being resolved (i.e. in the manner of a HoMM) and we get that the battle reports, in short we do not learn how the AI attacks us, in short, each time all my cities end up being captured and the AI is too hard according to me, even after 50 games to test different strategies.

Strangely if two players play on the same machine (I mean by that two human players), there the fights are solved at the HoMM (Heroes of Might and Magic), I would like to emphasis: why the hell didn't you just integrate this option against AI?

Or at least in the options, we could have had the choice to hide or not, the fights being resolved during the AI turn.

You will have surely understood it for me this Gold version is not worth it and I do not want to hear any more about it, nothing worse in my opinion, than not to take any pleasure has to play if a game is completely unbalanced and leaves no chance to the player.

I even tried in very easy mode but nothing, for me the game is unmanageable in solo and each time I ended frustrated by taking no pleasure, it was my only video game disappointment.

In the last thirteen years any AAA game is a disappointment.