Ricky_Bobby: Star Wars: Dark Forces - the platforming, especially
that part towards the end of the game. I rarely get this angry at a game.
Magic Carpet - the flight mechanics. I find it impossible to play the game regardless of whether I use a gamepad or keyboard/mouse, I think it controls horribly. The rest of the game seems really good though.
Darwinia - the dumb AI. Had the AI been just a tad more intelligent in the game, it would have been a great game, but as it is there's too much babysitting to juggle in-between trying to meet your objectives. Perhaps this has more to do with you having limited control mechanics, but still ... the enemy AI are really smart, yours are not.
Star Trek: the 25th Anniversary - the ship combat. The point & click part of the game was awesome, you could solve the problem each scenario presented in several different ways, leading to different outcomes. The ship combat made the game less fun to play, I almost dreaded the wait until the next combat part.
Albedo: Eyes from Outer Space - the overly obscure puzzles. I dig the surreal sci-fi settings, but most of the puzzles required out-of-the-box solutions where the logical connection between item A and B was too obscure.
J.U.L.I.A. Among the Stars - having to memorize story passages. I was not aware I had to memorize, or at least write down, certain passages from the texts I encountered. This lead to extensive backtracking as there were several of these puzzles towards the end of the game.
Meridian: Squad 22 - the dumb AI of your troops. As a whole I liked the game, but the AI was tricky to handle because they sometimes ignored your orders and often got stuck in the environment. Using the map for navigation solved the latter issue, but the AI made the game more frustrating than it should have been.
Dead State - the morality system. Despite keeping your residents well-fed and secure (!) they will rebel against you unless you can find the
one special item that each respective member craves for, things like luxury chocolate and whole-bean coffee. Not only will they rebel, they will execute you for it .... for not finding a bar of luxury chocolate (!). Thankfully there is a cheat against this bizarre game design choice, which I highly recommend you find and use.
Dark Souls - the lack of a manual save system. 'Yes', these games would be improved if you could save and load of your own free will. It would not detract from the challenge, it would make the games less tedious.
One has to wonder why any FPS made during the Quake 1 days thought platforming was a good idea. But even Half-Life commits such a sin.
On the matter of Magic Carpet, one has to wonder why the flight was so terrible when flightsims had been a thing for a while. Even Microsoft Flight Simulator was up to version 4.
As for Darwinia, isn't there a flimsy justification in that your Darwins are disconnected from the bad ones and therefore don't have full access?
The ship combat seems to be on ice. It's so slippery and I have to wonder how they could screw it up with it being simply to move the mouse and click.
Are we talking actual puzzles that just require esoteric solutions, like having to use a nanobending refractory to rearrange a tower of Hanoi, or something stupid, like having to trade a man for a rubber chicken with a pulley in the middle but only after answering obscure trivia about the Redsox of 1910?
This reminds me of a segment in Legend of Mana where you had to memorize a spell in order to save some lovestruck idiot who happened to serenade a pissed off half-basilisk. Screw up the spell badly enough, and he explodes.
I take it there were no tactical orders to give to your squad, like "Wait here" or "Retreat when health is low"?
That just sounds dumber than the Bethesda morality type system, which seems to rely on a binary switch you can fix by accident.
As for not being able to save in Dark Souls, I think that's part of the self flagellation system the entire game seems to base itself on. You are not
worthy to save, unless you solve a trial, or are otherwise a coward, the design says.