Maybe I didn't explain myself well. I don't mean that I thought the ride was literally a recreation of the Apollo program, and I understood the story element as you mentioned. But that still makes it a case of saying, "in the future...you will get to undergo the kinds of training you've seen astronauts do for decades!"
Here's another way to put it. A few years ago I got one of those official WDW planning DVDs. The theme that year was "the place where dreams come true" or something similar, and you had guests and cast members talking about how they lived out childhood dreams through the magic of WDW. Well, I might have had dreams about visiting a "Star Trek" space station, where you can sip a drink from an oddly-shaped glass, standing in front of a huge window, watching the star ships dock, as a hologram sings a warbling tune in the corner. I haven't ever dreamed of going through the kind of training that would make that possible.
Believe me, I understand how difficult it would be to make a realistic version of going to Mars. Instead I would have made a sci-fi version, so you're on a station on mars with glass tubes connecting different pods, and outside you see strange flora that resulted from mutations, hovercraft skimming by, etc.
But of course I understand that it would cost too much to have the current portion of M:S exist simply as a lead-in for a huge show set, regardless of how it was themed.
Just to be clear, although I don't love M:S, I don't hate it, either. It's just not for me.