Only 2 of those niggles were really bad.
The Memory/expanded memory, and autoexec.back/config.sys
The hard drive space is to be honest still a problem today (and much worse for poor console owners

), the IRQ issues you only really ran into when you changed hardware, and the copy protection wasn't a major issue (unlike modern drm..), and the cases are the reason I always buy a brand name now

(having left a blood trail in many an old machine).
I actually miss the old days at times, when games had to rely more on gameplay and/or story than how they looked with a quad SLI running 3d at 2048 pixels
I used to have about 20 or so boot discs for different games with different variations of the config/autoexec files loading different things into himem and extended memory

(I think I had 4 basic ones with different combinations of cd rom and sound card driver, then had others that juggled the basic settings depending on the game).
As for multiplayer...The joys of finding and installing one of the new enhanced RS232 cards that had the new fangled FIFO buffers and could work at higher speeds for games like Netmech and Duke Nukem 3d
