Going to ramble a bit more here. It's not too surprising that the first patch appears to mostly be addressing quality of life / balance type updates, as they can be knocked out quickly, but I just want to say again: Firaxis, please make the affinities distinct.
I think the best way to go about this is by analogy to another game. Let's look at StarCraft II (and StarCraft). There's obviously a lot of mechanics there that don't really translate to talking about Beyond Earth. However, I want to focus on how SC2 manages to differentiate the races *even in domains that every race must have.* In other words, a core requirement of the game is that everybody can do it, yet each race does it differently.
Movement: Every race needs to be able to have speed / mobility.
Terran: Their units get short-term, activated speed boosts (Stimpack, Emergency Thrusters).
Zerg: Their units are just naturally the fastest, and they get even faster on "creep" they can place on the map.
Protoss: They teleport. Most of their units teleport in, and lots of them can just plain zap somewhere else at short range, and no other race can.
Cloaking: Every race can play with an invisibility mechanic.
Terran: Their stealth units must pay an energy cost to cloak; when their energy (=MP) runs out, they drop out of cloak, and they're at least somewhat deep in the tech tree.
Zerg: Every single Zerg ground unit can "burrow" which makes them invisible, but they (usually) can't move or attack, unlike the other two races. Burrowing is free and can be done whenever, even for the 1 unit that can take actions while burrowed (Infestors).
Protoss: Their cloaked units are always perma-cloaked. No energy cost, they can just move & attack normally. 1 unit can extend cloaking to allies. (Protoss cloaking is also rare and far up the tech tree.)
Workers: Every race has a worker unit for their economy.
Terran: SCVs can repair each other at the cost of minerals, are slightly more durable than other workers, and are required to build buildings.
Zerg: Drones *turn into* buildings on creep, including enemy creep.
Protoss: Probes aren't required to hang around when warping in new buildings, unlike SCVs / morphing drones.
Okay, this is a BE forum, why am I rambling about SC2. Well let's take the same comparisons of core concepts in Beyond Earth for Affinities.
Beyond Earth Production: Every affinity needs a way to build stuff.
Purity - Boreholes are +5 Production, +5% prod rate (or +5% energy). LEV Plants suck but are theoretically +6 production if you can spare 2 Floatstone (protip: no); Skycranes are +15% production rate if you can spare 4 Floatstone and offer a Floatstone boost.
Supremacy - Bioglass Furances are +2 Production, +15% prod rate w/ a Firaxite boost that costs Firaxite.
Harmony - Biofactories are +3 production w/ tiny random other boosts, but require Petroleum. Microbal Mines are +3 Production & +10% production rate. Costs Xenomass.
...except EVERY AFFINITY IS BASICALLY THE SAME. Okay, the one part Firaxis got right was tying maintenance to the "affinity-specific" resources (even if these buildings are a fairly bad investment of such resources at their current power level, even assuming a trade route nerf), but it turns out that every affinity can get a small flat boost and a percentage boost off a building, with the non-Borehole ones requiring stuff. Let's see some identity!
Example fix:
Purity gets an identity as the "industry" affinity. They will dig up this planet with Boreholes and use human voracity to grab everything. They keep their current set, but buff it so you feel a noticeable advantage - especially the buildings that require Floatstone. ("Awesome, everything builds so much faster, Purity is great!")
Supremacy is okay with Industry, although such physical concerns are a tad beneath it. Maybe flavor it such that Supremacy gets big flat bonuses, but no percentage bonuses, and their buildings are energy-expensive to maintain? Supercomputers who aren't "creative" but are consistent or some such excuse. I'd also argue elsewhere that Supremacy could gain an identity as the "orbital" Affinity that likes to launch lots of satellites, so maybe make Geoscaping / Orbital Fabricators earlier in the tech tree and require some amount of Supremacy to build them, and use that for production boosts.
Harmony gets zilch. (Sorry, but with there being non-affinity specific buildings that grant production, this isn't TOO bad.) Better take +production boosts off other building quests. MAYBE keep the +Chitin boost Biofactory, but make it more well-rounded - +3 Production, +2 Food, +1 production / +1 Energy from Chitin say. Cut Microbal Mine. If production is so core to the game that Harmony needs to keep something, make it give production in a way unique to it - not a copy of how Purity & Supremacy do it. A building that grants +Production if at least 3 tiles within a city's borders have Miasma, perhaps? A building that offers a big boost for constructing Harmony-affinity only units/buildings, and nothing for anything else?
The same comparison could be run for many other parts of the game - Food, Espionage, Military, Workers/Terraforming, Affinity-specific Wonders, etc. The parts of the game that *are* different often aren't different in meaningful ways - is there really that big of a difference between Call Worm & Dirty Bomb? Oh, at least there's flavor here, but they're both just "mess up an enemy city". If you can have flavor AND distinctive gameplay, that's even better.
Lastly, distinctive gameplay also inherently adds to the *conflict* inherent between the affinities. Purity is pro-terraforming, Harmony is anti-terraforming. Let's see some sparks! Give Purity special bonuses with Terrascapes (move it out of Prosperity?), give Harmony special bonuses for tearing Terrascapes down or sabotaging them. Supremacy is all about robots & AIs. Give them a special weakness to enemy intrigue that allows Purity spies to subvert or corrupt their systems, and Harmony spies to crash them. But let Supremacy have something neat from it - perhaps thanks to their buildings all being rebalanced to offer big flat bonuses, Supremacy can settle in harsh environments that'd scare off Purity or Harmony like Tundra and still get something from it, who cares about such piddling concerns as temperature. This is already in BE very minorly, but play up Supremacy gets Satellites, Harmony shoots them down with a Rocktopus or the like. Harmony... just give them SOMETHING cool with the aliens, and have Supremacy & Purity hate & fear them for it. They can also be part of revamping what Health means for each Affinity - Harmony is healthy because they adapt to the environment, Purity is healthy when they adapt the environment to humans, Supremacy doesn't care about health but shrugs off the downsides better 'cuz robots. Mechanically, give Purity cities big health penalties if they don't clear Miasma out once you adapt Purity, but bonuses for Terrascapes? Then do the same in reverse for Harmony, they get Health off Miasma and can now troll Purity by launching Miasmic Condensers? Supremacy, yeah, just shift the scale such that they hit low health / high health tiers at higher numbers then everyone else - say -40/-20/0/20/40 rather than -20/-10/0/10/20. Encourage you not to care as much about such trifling matters. (If you're worried this is broken, well, fix that elsewhere.)
Another option to add replay value: Make Affinity combinations something real. Domination & Contact don't require exclusively beelining one Affinity, so consider tempting people to build 2 Affinities at once. The different upgrades - Evolved Battlesuit, True Battlesuit, etc. - just plain don't matter enough. Create a building that requires 4 Affinity in each of *two* different affinities, and make it very powerful (and flavorful!). Get people tempted by it to maybe not beeline as hard as they do now, or at least offer something interesting for the Dom/Contact player. Maybe create a 5/5/5 building too, for the truly crazy player. You've just gone from 3 basic ways to play to 6 or 7.