Half Life, Rise of Nations, and Call of Duty

None of these are indie games. While the teams were a lot smaller than modern AAA, they weren't one or two people making a game in their spare time the way many indie games get made.

Pixel art games are popular for reasons including being much easier for solo devs or small teams to create. It cuts out a ton of work like rigging models, in many cases dealing with physics, complex lighting, and all sorts of those things. Depends on the game of course, but in many cases a lot of that stuff is either a non-isssue or way simplified. All art assets can have a unified look and quality without taking forever to make.

Games can also be lightweight on needed specs to run. Again helpful for solo devs or small teams which might not be optimization experts, and it means much less of having to figure out how to help people having issues on all sorts of hardware combos.

Pixel art can be easily readable on small screens pretty easily, which is good for things like playing on a Steamdeck. Again, plenty of non-pixelart games are readable on screens, but it is certainly easy to do it in that style.

This isn't to say non-pixel art indie games don't exist. There's tons and tons of them. I'm pretty sure something like 50 trillion indie games are released on Steam every picosecond. There's plenty that do the late 90s-early 2000s aesthetic. Or you can just play old games on Steam, especially ones that have gotten official or unofficial quality of life improvements since their release.