So the strangely semi-sentient whirlstorm at the beginning, which reveals the aliens' hidden base, is an old welcoming program? Why the hell did the aliens create a welcoming program that rips people apart or violently launches rocks at them?
It was revealed to be not a welcoming program, but a security check: it asked them for a password, which the humans didn't realize it was doing, and they gave the wrong answer. So it moved to safeguard the message, as it had been designed to do.
So, given that the Native Martians knew that there was life developing on their neighbouring planet... who else did they expect would show up? That they're revealed to be benevolent doesn't explain why they would design a message of peace only to sic the dog on the poor dopes that stumbled across it. On the other hand, it's entirely possible that the watchdog misinterpreted the scanning as a hostile action.
Continuing that line of thought, it also conversely may have acted as a Secret Test of Character to see whether humanity was a species curious enough what happened and brave enough to attempt to mount a rescue of any potential survivors. It's a bit morally reprehensible if so, but it could just be their alien way of thinking.
If they [the aliens] originally seeded all life on Earth, why didn't they simply colonise Earth instead of heading to another galaxy? Of course, one could argue that living in sight of their destroyed home could have been too painful.
That decision may have had more to do with practicality than anything else. Say they go to live on another planet, but it turns out to be doomed in some fashion as well. Sending that DNA to earth would be like doubling their chances, so to speak.
Two reasons present themselves: 1. Earth before the rise of lots of complex life was a very different place, with no real ecosystem to speak of, so it's entirely possible that the young Earth was uninhabitable, and/or; 2. The realization was made that the Earth, too, would be subjected to significant impact events (which it later was), so rather than building what amounted to a doomed colony, they decided to strike out for greener pastures elsewhere.
Assuming both Mars missions used ships of the same class, does this mean that the return voyage to Earth was always meant to be in zero-g?
As we never saw a successful orbital insertion and/or landing sequence, it's possible that the engine section of the first expedition was still in orbit and awaiting recovery of the landing module. That way, the landing module would only require fuel for insertion and return to Mars orbit, rather than that AND transition to Earth.
How did the hologram know what the humans and mammoths looked like? How did it know what Earth looks like now with industry covering it? If it was watching the whole time, why did it need a security system?
It's been millions of years. Is there even a culture left at the place this spaceship is taking Jim to?
Many people who have posted discussions, reviews, and just plain complaints about the movie say something to the effect of "if the tether had been another 10 feet longer, Woody would've lived!" No, they both would've died. Terry had barely enough fuel to get back to REMO herself. Had Woody caught the tether, much of his inertia would've been transferred to her (he's heavier), meaning that she would've needed enough fuel to brake their combined mass and then accelerate it back in the other direction. Odds on, they both would've done a cannonball onto Mars.