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No one else mentioned this, but what if you color coded the eras since that is the primary distinction. As you said, people may just want to read military SF so, regardless of which number sequence you use, say you color code The Crypt era as red. That makes it immediately obvious to even the slowest student that the two reds go together. You could even color code the timeline. Or if you prefer you could color code by major groupings. Say purple for things related to Ancestor & Blue for things related to Infected.

The major limitation here is it becomes useless if printed in b&w, but I got the sense that this tagging system would be employed mostly on covers & the web so the b&w problem shouldn't crop up often.

As for the numbers themselves, I think the date system is probably the best. It naturally groups like things together. As for the associated cons I would think they were fairly minor. The majority of readers would understand the flashback technique and as for simultaneous events if the fact that they are occuring together is relevant I have to feel that would be referenced in the text. For people who want to get they're geek on the fully detailed timeline could be made available online.