Disclaimer: I am very, very new to Sims 4 so I'm probably missing something. Does anyone have any tips on how to give the aliens a fighting chance? Between all of high value rewards, the upgrades which require a ton of skill building and/or time in the scientist career, and the whole 'must marry an alien' thing, it seems like the odds are stacked against them when competing with the other options.
I haven't got very far yet, just to the birth of two of the first heirs and the marriage of the third founder, but I don't think it's as hard as you think. If you're more used to the other styles of play represented in the retail or mansion building option, those might be best to go with though.
I've chosen to do three sets of aliens, because I love them. The trickiest thing was I started with three male aliens, which was probably a bad idea since I had to find three female aliens or hope for abductions. Keep the genders balanced and make a few spares (I believe spares are allowed to marry into the other bloodlines, but I will check that again before I do it!), and make sure someone in the household does the scientist career not just for the gadgets but because when you get alien visitors to the lab you can make a note of their names. If you have trouble meeting them again then coming back from Sixam can give you the option to bring people back with you to your house, even if you didn't spot them there. That's how I just found the third wife.
Invite some helpers in, get one painting, maybe one gardening and another in the science career until they get to the cloning machine at least, use their points from doing aspirations to keep your aliens in moodlet solvers and speed them through their careers and their own aspiration, rocket building and the rest, and it shouldn't be any tougher than the other options.
If you haven't already, reading some of the tournament challenge winners talking about how they kept their moods high, completed aspirations, made lots of cash and finished careers quickly should give you more ideas. Also check out the dynasty stories that have already started so you can see what people are doing.