The addition of pets has put a decent amount of importance on the base building and cooking mechanics where previously there was none (at least, for my group).
My friends and I aren't people who are big on base building or cooking - we're mostly here to shoot stuff, not place boxes symmetrically or bother with digital busywork. For the longest time our "base" has just been a bunch of deployables and storage boxes strewn across the Office Sector cafeteria security office where we started. The most base prep work we've done is getting a 8-slot planter down and filling it with potatoes to solve our hunger issues. When it came to Assaults, we'd usually just take them head on in the open without static defenses or walls. When Cosmic Companions came out, we toyed with the pets a little, and while they're kind of a meme in combat, they were cute enough that we all started collecting them in the cafeteria seating area, beginning a chain of events:
The cafeteria was way too open for pets and they'd eventually roam out the front into the Office sector lobby, then either find their way to Cascade Labs or get murdered by the Security Bot at night, so we spent some time workshopping an automatic door system (having to actually farm a few things) that would prevent them sneaking out. Then it was getting hard to feed our main pets their bigger meals without another pet stealing it, so we eventually put some proper stables up. Then of course we had to decorate their little enclosure, so we spent a bit finding decorations in cleared areas.
At the point the update came out, we were clearing the >!Mist Reactor!<, and the pets seemed mostly fine there. Once we got to >!Cloud Reactor!< they were getting shot to shit or exploded every 15 seconds, so we committed to grinding our Cooking Skills up to feed them better food and speed up their leveling. We put another planter down to churn out Cosmato Space Wraps (the biggest food item we could make) and Anteverse Wheat, and every morning someone makes a trip to >!Dunkeltaler Forest!< to nab the respawning Hamburgers.
We were still clearing Assaults out by hand (because they're easy enough even on Apocalypse), but eventually we hit a double >!Corrupted Bot!< raid. We already struggled with the >!Corrupted Bot!< in the >!Mist Reactor!< area and two at once was more than we could deal with reliably without preparation. They tore through the Carbon Barricade we had blocking the entrance to the pen (it was fine for every other Assault but this one) and managed to kill almost all our pets before we could stop them. Following that, we spent an entire session of redesigning our base, farming up resources to set up better defenses (Lightning Coils, Laser Turrets, Shock Traps) and barriers (Carbon Barriers, Hardlight Drop Shields, Wooden Barricades, and Cement Bags all buffed with Eye For Detail) to keep the pets safe and prevent Assaults just murdering everything again (which we just had to improve again recently as some >!Witches!< flew over the railing into the pen and burned some of our lower level pets to death). The doors leading to the pet pens now has two loaded Rocket Launchers mounted on the wall as a kind of 'break glass in case of >!Corrupted Bot!< raid' type deal, and now the higher level pets (our main lil guys) are stored up front to take the brunt of the fighting if there's still a breakthrough that makes it past all the defenses (somehow).
I feel like we wouldn't have bothered with any of this if we didn't have silly little guys to keep alive, and in that manner, I think Cosmic Companions is a pretty good update with how it ties the game's systems together more or less by necessity. Kinda wish there was a trough or something though I could fill with food that the pets would help themselves to as they got hungry, so I didn't need to hand feed our 20 something pets, but still, enjoying the update thoroughly for all its brought to our experience.