Quake actually has a really good segregation of duties between the engine and the QC code - I've heard how much harder it is to decouple gameplay and visual modifications in DooM. A good example to have in mind is the total conversion Malice, which replaced every graphical and audio asset in Quake, with completely different enemy behaviour and gameplay. All of this was accomplished without any modification of the engine (it predates the source being published).
There are some places where changes are more difficult/impossible to make, like the HUD or the fundamental physics or the rendering of surfaces. But if you want a monster with all new animations, behaviours and attacks, that's easily in reach of QC.
It's a shame Inside3d has been hacked, as that used to be a good place to start. However, the best resource for a new coder who wants to modify monsters is AI Cafe, and although the original site is long gone there's a mirror at:
http://www.quakewiki.net/archives/aicafe/tutorial/main.htm
Although I love promoting my own site, unfortunately it's pitched at the vanishingly small "experienced QC" crowd, so go do the AI Cafe tutorials first.