And the aliens are integral to the point of the film, which is that it "updates" the movies it's referencing to match the era it's representing. (I read somewhere that an earlier title considered for the film was "Indiana Jones and the Saucer Men from Mars" -- a phrase Jones actually uses in the film. I think that's a much, much better title than the one we got, and it would've cleared up a lot of confusion.) I've said it before: I actually prefer Indy 4 to either of the earlier sequels b/c it's the only sequel among them that, because of its shift forward in time, is explicitly "about other movies" (in this case, sci-fi, Cold War scare, and biker films) in the same way that the first film was.
Nor am I arguing for the "greatness" of the film or whatever. Plenty of flaws to discuss -- but more egregious than the those of the earlier films? Nah.
Personally -- and I have no idea if this has been discussed extensively elsewhere already -- I think it's both a structural flaw and a missed opportunity in the film that Jones is set up to be under suspicion by the Feds early on, and then that plot thread is dropped. I think it would've really opened up the film if *both* the Reds and Feds had been on his tail throughout.
I definitely agree that an ongoing dispute over command of the base would really help the series. I've long thought that that was *the* obvious narrative step the original series never took, which is a shame, b/c then the series would have had some sort of credible dramatic focus. At least in the premiere episode, it looked like the character of... was it Simmons?... was being set up to play foil to Koenig, but he was promptly killed off.
I also quite like that photo of Ripley, above.
It's a mistake to be distracted by the "coolness factor" of a moon base, or by pie-in-the-sky "it'll produce fabulous wealth" schemes. There's really only one reason to put humans in space, and that's to live there -- or as an interim step, to figure out if they can live there. Maybe a Moon base would be useful for that interim step. Either humans *can* live in the reduced-gravity environment of the Moon, or they can't. And if they can't, then that's it for living on the Moon. (And possibly that's it for Mars too.) But you don't even need to go to the Moon to get an answer to this question: you could just set a torus-shaped station spinning in orbit at Moon-gravity and watch what happens to the crew.