I'm not sure I'd go with the "aliens increase stats over time" method--doesn't seem to make much sense without lore behind it.
Rather, what I'd like to see is a sort of randomized events that cause monstrous problems focused on alien life-cycles. I.e., I'd like to see random hexes with miasma have a percentage chance of biological disasters:
(1) "Nest Upgrades": If a nest hasn't been cleared by x turns (+/- random number), the nest upgrades to a spawning ground. It develops a ranged attack, develops a chance of spreading miasma to a random adjacent tile each turn, and the number of aliens it produces each turn increases. The Upgrades come in different flavors--one for each alien species--so one type produces manticores, another drones, and so forth. However, the new aliens are significantly tougher than the old one--maybe +50% hit points and +50% attack damage, and have some different color or different markings to make them distinct from non-upgraded examples.
(2) "Mating Ball": Just as many snake species form mating balls, in which dozens or hundreds of males show up in the presence of a female, we could have as a random event an uncontrolled nest have a percent chance of turning into a mating ball for siege worms. The nest undergoes a visible metamorphosis of some sort over 5-10 turns (to give players a chance to deal with the issue), and at the end of the metamorphosis, 2-7 siege worms begin migrating toward it--all of them with heightened aggression as they seek to mate.
(3) "Cocoon": The designers could pick two or three species of aliens randomly each game as those that pupate. If these species of aliens are still alive at turn 200 (+/-10%) without being wiped out, they pupate over 30 turns and become something similar to Xeno-Titans, but computer-controlled and hostile. If players find the cocoons before the metamorphosis is complete, they can wipe them out easily enough. If they hatch, there's a whole new problem to deal with. I imagine this being particular relevant on unoccupied continents/islands that players neglect. This might add an element of danger to late-game colonization of new unexplored areas. Without these metamorphoses, there's little danger in trying to set up shop in new areas. It also provides an incentive to explore new areas thoroughly late game. Any unexplored areas with nests will potentially be generating cocoons.
(4) "Hundred Year Migrations": We already know that Kraken tend to cluster together in late game. Perhaps very so often they act like salmon and migrate upstream--coming onto land!
(5) If aliens are less of a threat late game, perhaps late game after turn 200 is the time to throw in a few random cataclysmic events--tornadoes/hurricanes, meteor strikes, volcanic eruptions (that create new Canyons and Geothermal resources, but which destroy worked tiles), meteor strikes, landslides near mountains, tsunamis, and terraformation disasters, for instance? Perhaps certain wonders like the Tectonic Anvil or certain technologies like Weather Control satellites might grant immunities to these cataclysmic events? I'm not sure making aliens tougher is the only way to make the late game challenging--maybe the planet could show its inhospitable nature in other ways. I would find it interesting if these disasters actually changed the terrain tiles in some limited way--it would just be a design challenge to do this without making the outcome unbalancing and random, but still interesting and challenging.