Whie "protectionism" might be very difficult to program into the game, I for one would welcome Harmony being able to do something with the aliens.
The thought of using the aliens to wage a proxy war sounds amazing and their is a mod that allows aliens to attack cities and outposts but even when given the option to do so, aliens rarely attack city tiles or pose a credible threat.
I farm them for science now in my games and only because I am taking that tree anyway as the science quickly tapers off ALA culture from barb kills in Civ5.
I could see protectionism take the form of an agreement to both not attack them and to fight Aliens near them, with perhaps their opinion of you changing based on how good of a job you did.
It would be tricky, but I'd love to have the option to ask for and offer protection from Aliens in deals.
Of course, about half of the AIs should probably take the "Stop killing Aliens, it is dangerous/ unethical" route.
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For Harmony my ideal would be mid to late game Aliens swarming the cities of those they are at war with, with their combat capacities upgraded by food-providing trade routes to nests.
If they could be a real threat it would give Harmony a gameplay reason to want Alien populations to thrive and for other Affinities to be concerned about it.
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What mod is that?
In my experience the most threat Aliens pose to cities is the occasional Siege Worm or, in one rare case, two spawning unusually close to one.
Even then it is extremely difficult to anger the Aliens without some mod altering their thresholds - I made one such mod myself in the steam workshop.
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I'm okay with the boosts for killing Aliens tapering off, but if Aliens were truly more of a threat I'd like to see greater early rewards.
Early Might could become the virtue tree of getting a potential jumpstart for your colony by killing Aliens.
The Energy from destroying nests could be changed to a substantial Food boost in the nearest city, and the Survivalism virtue could similarly give food equal to their combat strength.
Generally I think bonuses requiring active play should outshine passive ones.
The primary cause was Staggered start of the AIs, especially on CD release. (AI bonuses were increased on the first patch for the highest two difficulty levels.)
Basically for the CD release, the AI wasn't getting as much from the stagger bonus as it would have had naturally if they had landed on the same turn the human did.
A secondary cause is that humans are much better at optimizing tech research on the tech web for their chosen victory condition than the AI, but that was already the case for Civ V.
As a Marathon player, I wish the AIs spawned considerably later with more time between with more formidable bonuses.
They seem to all drop in almost consecutively before I've had time for much more than the earliest of exploration ventures.
Imagine if, say, an AI dropped in with a considerable army and a hostile disposition - how that could shake the game up.