I'm not saying there weren't good games but the perception of how horrible those years were is entirely dependent on what sort of games you want.
If you're the type of player that gravitates towards shooters and multiplayer games, or even cinematic experiences like jrpgs of that time, those were probably great years, but for those players, like me, that look for complex and systems-heavy games, like crpgs or immersive sims, or genres historically associated with pc gaming, like P&C or strategy games, those were awful years with barely any relevant release, and those that did exist were watered-down and dumbed-down copies of greater games that released in the prior decade, that needed to be that way in order to be playable in consoles. I'll never forget nor forgive what they did with Deus Ex's sequel and that was, chronologically speaking, one of the first signifiers of all the dreadful decisions that were to come.
Thankfully we're past that and, while trend chasing is still very much alive, now everyone is being catered to and the whole ecosystem is healthier because of it, although I still wish there were more crpgs and TB tactics games being made.
There was a huuuge change in a lot of popular PC games (and some new ones taking over like MOBAs), but while there's definitely a part of multiplatform development affecting some games and limiting them a lot (the Xbox is particularly to blame here, Microsoft sabotaging Windows to expand to consoles, or MP3 players, or mobile phones and whatever else that one exec thought about before leaving with their golden parachute is nothing new), and the now very well known game sellers defining what was supposed to sell well and what wasn't (and how wrong they were and got steam-rolled)...
There's also an aspect of genre fatigue, not everything can stay on top forever. I'm one of those players that got bored by samey RTS games releasing by the dozens from 1995-2003, and was less and less interested in them over the years after spending thousands of hours in them.
Now why point and click suffered that much, I'm not completely sure, but there were some European series hanging on, so maybe it was more that they were abandoned by historical developers instead.
Because that's the real reason why so much of the PC landscape sucked so much; tons of devs switched for games in either different genres, or just ones that would now use full 3D rather than the old 2D.
A lot of those conversions failed hard (and not only for PC, but also on consoles, lots of companies that keeled over in the early 2000s by losing sight of why they were liked, like Rare), and a lot for others... well that's something that I felt back in the day, but was apparently not in the majority: games that weren't simplified because of consoles, but because full 3D is much harder and much, much less prone to player possibilities (and would also take much longer and faaar more money than 2D, starting that visual war that's just slaughtering the entire AAA industry now).
I know it has tons of fans, but for me going from Baldur's Gate 2 to Knights of the Old Republic and Jade Empire (and even Neverwinter Nights was worse) was a heartbreak.
Dialogue? 90% is gone.
Exploration? We're in 2003, say good bye to the big open areas with fog of war, say hello to tiny, empty maps with almost zero interactable elements. Build customization? Fuck that one too, it's not like we can add the equivalent of 200 spells that were only tiny sprites back then.
Just follow the story and be happy. The beginning of the end with "cinematic" replacing gameplay.