Irons' co-op script
adds several features to the base co-op play, including ammo sharing and teleport beacons. If you try it, use the version here
which fixes an important bug.
Marathon A1 interim was a port of M1 levels to the M2-based Aleph One engine. This port has several differences from the original Marathon, mainly in enemy behavior, so I wouldn't recommend it but some people that played it first prefer it.
M1A1 was the original port on which "Marathon A1 interim" was based. M1A1 contained extra secrets and levels which were never in Marathon, along with various porting errors in enemy and ammo placement. Marathon A1 interim was a "cleaned-up" version of M1A1 more faithful to the original. Aleph One 1.0 included Marathon A1 interim; 1.1 included original Marathon but no co-op; 1.2 and 1.3a1 include original Marathon and co-op. M1A1 was never bundled with Aleph One.
The original Marathon did not support co-op at all. This leads to some annoyances: for instance, there's only one fusion pistol in Cool Fusion instead of one for every player. I would recommend irons' script because of the weapon and ammo sharing, so the two of you don't have to fight over new weapons.
Nobody has mentioned those M1 co-op bugs before; I'll look into them. Does 1.2.1 work fine?
Unfortunately, it's not possible to revert to a previous save in co-op play. You have to manually quit the game and continue the save from the main menu.