1) Technology continues to soar upward which allows game developers to make 'Graphic Rich' games that cater to a society that favors progression, not more of the same. In 2013, Quake to many looks like an outdated game (Graphics and genre wise) where people in general prefer the best games available which equates to 'Realism.' Quake is not realistic and some claim it to be 'cartoon like.'
2) Now that game developers have the ability to make 'life-like' games, the community followed suit because it was the natural progression.
3) The market switched to 'Open-Environments' that you see in military shooters like COD or BF3. Quake is a 'tournament-arena' game that was played out in the early 2000s, the market got bored and moved to 'realistic environments.'
4) ID software has made zero effort to modernize quake 3 for the ever progressing market place. If a company doesn't consistently innovate based on market conditions, their product becomes obsolete... that's what happened w/ Quake. Quake's only chance at this point is Quake 5 that is made for the market, not an extinct genre.
Look at Kodak for example... they dominated the market place for years because of 'Film based media.' They didn't switch fast enough to memory cards and lost the bulk of the market place because of it.... they didn't adapt, so they got left behind.