I dig up this thread, as I have several ideas about aliens in game. I feel alien design is the biggest problem in Beyond Earth. Game is about colonizing alien planet and all planets we can land on are basically the same planets with differently shaped and colored lands. Biosphere is absolutely identical everywhere. Playing it I have feeling that all planets in the universe except for Earth only look the same. And it is bad.
There should be several completely different types of alien NPC players, not only these crustacean-like, which guard their nests in Beyond Earth. This type of alien biosphere (lets call them type 1 aliens) should be only on some of the planets. How alien wildlife could behave? I describe some possible other types:
Type 2: No nests, simply several species roaming freely on the planet. They are not spawned by nests but run on a planet surface and each unit can replicate itself in special condition. For example herbivorous species unit could replicate themselves if it spent for example 3 turns in forest tile. Or small rat-like pest species should replicate just after left not attacked for 2 turns. Carnivorous species could replicate if it managed to destroy certain number of other units (alien or human). These aliens would not guard nests, but some species could be aggressive. Also, when aliens behave this way, some species can be totally eradicated if are just hunted to extinction. But if some species was eradicated there should be some negative consequences, for example if you made carnivore extinct, you must use your military units to kill herbivores, otherwise they will be everywhere. And too abundant herbivores could destroy farms and plantations or something like that.
These aliens could look different than those from Beyond Earth. Maybe they should be zeppelin-like air floaters? Or long snake-like legless crawlers? Or creatures with radial symmetry similar to brittle stars?
Type 3: No animals, just aggressive plants. If left untouched they will expand to neighbor tiles and potentially cover entire map. When attacked they emit toxic gas 1-4 tiles from themselves depending on how big their group is. Bigger group produces more toxin and also it inflicts more damage per turn. They should be destroyed quickly as they would become very dangerous when their group grow numerous enough
Also these could look weird, not exactly like earth plants, maybe like gelatinous ocean from Solaris, or coral reef, or alive stone pillars.
Type 4: Single dangerous animal species on a planet. They live underground as larvae for example for 15 or 20 turns, then emerge in great numbers at random locations as adults, attacking everything around them (themselves included) and all die after 5 turns.
Well, this sounds like some weird hybrid of mayflies and Pitch Black monsters.

Players on world like that would be forced to outlast each wave.
Type 5: Single species of Godzilla-like kaiju aliens (maybe owners of these giant natural wonder skeletons, each one 4 tiles long). For example there should be only 10 or 20 such creatures on a planet. They should be almost unkillable (they should be possible to kill only with about a dozen late game units and with big loses in army which attacked them). They of course could not be aggressive (as surviving game would be impossible), but they would damage tile improvements and kill units when they walk on them grazing peacefully, but each of them would attack back with tremendous city-razing force if attacked.
Type 6: Ant-like aliens guarding few nests on a planet, but guarding it very aggressively. If your unit enters borders of their territory (which are invisible to you and expand far beyond normal unit visible range) all units from this single hive would attack intruder. If you trespass their territory several times, their armies may begin to raid your cities and kill your units outside their borders. Their hives don’t cooperate and often two hives could fight their own war.
Etc. On every planet there should be only one random alien type from list like that. There could be many different types of alien wildlife and in Beyond Earth on every planet there are the same aliens. Well, probably most successful species in galaxy. They will certainly colonize Earth soon.
Also there could be sentient alien civilizations. True enemy opponents, even if they would be NPC, not just “barbarian” wildlife. Maybe even several alien races, each with unique appearance, unique units, buildings and tile upgrades (most would be not useful to humans and other aliens, but some if conquered and incorporated into your territory could provide very rare bonuses). But they could behave weird and irrational in our human point of view.
For example alien civilization could:
Berserker alien civilization- these are in permanent state of war with any other player without any possibility of peace.
Brawler alien civilization – These have weird understanding of honor, sparring with nearby units without possibility of starting war. (“Well, they just killed your tank, but it was just friendly brawl, you can also kill their shriekers and they would not get offended”). Also you could still trade with them, even if you cannot be sure if they would not kill your convoy next turn
Silent alien civilization - These are impossible to communicate with. Simply their language is completely untranslatable. You cant trade with them, if you attack their unit, they would understand you declared war with them, if they would attack you, you understood they probably declared war with you. If they don’t attack you, you can guess, you have good relations with them. Also if they were attacking your cities and then stopped and went their own way, you could guess, they now have peace with you (it doesn’t mean you cannot attack them if you want).
Ignorant alien civilization – You would be invisible for them until you attack them. They would ignore your borders and could place a city even on tile adhesive to your city and start to upgrade tiles with their own alien upgrades, each would reduce tile income to 0 in your city. If you would attack them they would fighting with you until either you or them would be eliminated from game. This opponent would be very annoying, especially if it would have strong army.
Abyssal alien civilization - They build their cities only on tiles of deep ocean floor. If unprovoked they never go outside water, as land tiles have no value for them. But if you are in war with them, their army can fight also on land.
Of course alien city cannot be puppeted or captured, they are always razed (sometimes they may turn into precious tile upgrade). It happens also when aliens conquer human city.
Aliens armies could also behave strangely. For example move only every second (or third) turn, but, each of their unit would move (and possibly attack) two (or three) times during that turn. It could be explained that they are capable to boost their metabolism for short time, when they can move and think very fast, but then they must cool themselves while being inactive. Fighting with army, which behaves like that would be weird.