Well, If you make System Shock on Doom engine, remove the RPG and minigames, switch to checkpoint saves and linear level progression, but leave the complicated architecture in you'll get something close to Marathon.

From the short time I've had playing it I can safely say its MILES away from Doom....more along the lines of SS1, definitely...

Addendum:

Just replayed the game (first Marathon) and it's even more mediocre than I remember. This is a prime of great ideas wasted on a dull game. Let's see:

The good:
- recharge station
- story-driven
- terminals
- weapon has to be reloaded

The bad:
- enemies are dull and unimaginative not to mention a snooze-fest to fight
- the story has no actual impact on the game
- HORRIBLE map design - mazes everywhere.
- the game uses levers to progress which in my book is even a step below key cards (at least you feel you've achieved something when you find a card)
- the weapons are utterly crap and looks even worse
- the atmosphere is ... clinical and just doesn't inspire you at all
- you can't manually reload!
- AI is terrible - half the time, enemies die without even putting up a fight. Enemies that use projectiles run TOWARDS me! How does that make sense?

Really, I'd much prefer most early PC FPS over this.

We already have a thread about this.

Right here.