"One system that works incredibly well and has not been duplicated since is the Marathon series of games' "Pattern Buffers"."
Nice to find another Marathon fan in the wilderness
I prefer the pattern buffer idea to the auto-save checkpoint system that you find in games like Halo. You still have control over when you choose to save and you can do it as many times as you want, but you have to earn the right to save the game by fighting your way through to the next buffer.
Actually Planetside has something kind fo similar where you can access a matrix panel at any base and that will record your DNA so you can respawn at that location if you die - however since the game lets you respawn at any nearby base anyway it hardly seems worth the effort.
Interesting that Half Life had health temrinals like the ones in Marathon. Marathon had lots of firsts I think. The first FPS to have secondary triggers for some of its guns (like the assault rifle with the built-in grenade launcher). The first to allow full mouse-look for aiming etc. And it had such a great story too... sigh...
The other thing about Marathon which I haven't seen repeated is that it was seamless. No jumping forward a few weeks to the next setting, no hopping into a vehicle and switching to a cutscene as it takes you somewhere. The teleporter meant that every moment of action led straight into the next. Finished clearing out an area? Durandel says 'fine, now we need you over here'
Well, I'm sure there will be a Marathon mod for HL2.