Quite a lot of things, really. It's surprising how many things have not aged well in gaming at the time, if we just took off the nostalgia glasses.
There were quite a number of games that had either a lot of loading screens or those that took longer than it should. (Sometimes both) If you were lucky, they might have some interesting hints or lore to ease the wait at least. It still exists now, but consider how big games are now compared to then, and even the former usually isn't that egregious.
More so in handhelds and gimmick consoles, but shovelware was ridiculously common and simply hard to avoid, particularly with movie based tie-in games that usually was rushed to cash in. (Granted there were quite a few exceptions that stood out, but that was few and far between.)
I honestly find it amusing that people are bitching about localization being "bad" today, where in the early 2000's and before, localizers were actively trying to whitewash a lot of Japanese things in Japanese games, with the partial exception of Squaresoft and Capcom games. Japan and America in the 90's and 2000's had a quite odd relationship with each other, where we liked certain things or aesthics, but at the same time tried to downplay or outright dismiss their origin as being "too foruinn" for kids.
(It's one thing if it was due to dancing around copyrights like with JoJo or Resident Evil, it's quite another where entire characters and plots were altered in simply lazy ways, like with the first Persona game on PS1.)