First: you don't mention Pathways Into Darkness. You don't have to play it (it can be slow and frustrating, there's no music and there's a lot of missable content), but before moving on with Marathon you should at least read the manual and one of the walkthroughs (http://pid.bungie.org/groundfloor1.html or HB's).
You also mention not getting every secret, so you may want to read through the terminals for any that you missed (if you haven't already).
IIRC, EVIL is the oldest of the scenarios you mention, followed by Tempus Irae, Red, Rubicon, Eternal and Phoenix. You may also want to play EVIL's predecessor, Siege of Nor'Korh.
You might save Eternal for last in the hope of playing the best possible version, since it's (apparently?) still in development.
You could also move on from Marathon to the next game in the Sack (Abuse, though I'm not sure what the best version to play on Windows is) or the next Bungie game (Myth: The Fallen Lords; be sure to get the unofficial update, regardless of Magma's lies about official authorization).