probably the unhinged creativity and honesty in the content and styles of the sites. although web technologies back in the 90s (and to a lesser extent in the '00s) were relatively primitive, it didn't stop many webmasters from creating whatever the hell they wanted with whatever fugly css they wanted to use. we really lost that expression of creativity when people flocked to social media, since it tends to enforce uniformity across profiles.
i also believe that Flash was a great technology which Adobe should've kept alive. unfortunately, Apple pretty much single handedly killed it when they omitted it from the iPhone and their other iToys. i guess we have Scratch (and especially Turbowarp) but Scratch/Turbowarp don't have a proper standalone desktop or web runtime (like not even a script which can be plopped into ur page to use the runtime. and even if there was, you wouldn't be able to rely on it being present on most devices.
sure, web technologies are incredibly powerful nowadays, but... oh boy is Javascript a heap of SHIT. i love how lean .swf files are. it's similar to mod trackers where instead of downloading a massive rendered video, you just download a light-weight file with all the assets necessary to render and animate everything in real time. plus, Actionscript encouraged some creators to add interactivity to their flash files. as an example: i'm pretty sure that Troubled Windows has a section where you can close error messages which keep popping up.