You're looking for stuff that was a big deal but wasn't listed as a major feature of a new expansion, yeah?
I skimmed back through the patch notes to the 5.0 release, here's the big stuff that jumped out:
Salvage and reprisal were big changes to the base game.
There was the great 'Divide health and damage by 100' change.
There have been MULTIPLE iterations of the 'homeworld assault counter-exo' mechanic; didn't exist, then launched exos whenever a core guard post died, then launched those exos but from the attacked AI homeworld, then the current system is that you have 10 mins to kill the homeworld once you start or a BIG exo launches.
Champions got a new champion-nemesis exogalactic strike force response, as well as threat and defending nemesis responses. And an alternate progression mechanic, which is hugely popular for people that have played the same nine nebulas 800 times.
Carriers got totally overhauled; now if you damage a carrier, it damages the ships inside, and if the carrier is empty it despawns. That's a HUGE improvement over the old version where a dying carrier would merge its carried ships into... interesting things to avoid the ship count on the current planet getting too high. Oh, and carriers do more damage the more ships they contain.
Bullheaded targeting: carriers and some other things go straight for your fortresses and command stations, ignoring everything else.
Threat logic: the AI is now very sneaky about attacking you when your military force is far away or occupied in battle, or if your planets are already under attack.
Warheads got changed from 'X damage to everything within range' to 'X damage total, capped at Y damge per target', and you also can only build one per minute. That was a huuuge balance improvement. By which I mean, a nerf to Kahuna and various other masters who were otherwise unstoppable.
Reinforcement and wave logic were both heavily overhauled; they're both now based on strength budgets which accumulate over time, reinforcements track debt per planet, at high AIP reinforcement strength gets redirected to waves which is freaking terrifying, etc.
Golems got rebalanced (no more attrition, gigantic buffs). Spirecraft also got tweaked; siege towers and ion blasters became oversized plasma siege starships and translocating spire railclusters, which are both amazing to have on your side.
Special Forces got Riot Control Starships (and there was *much* gnashing of teeth). Somehow, this is Faulty Logic's fault, even though he didn't inspire this on purpose.
Astro trains got totally overhauled and are a colossal pain in the ass now.
Map untangling!
Batch auto explore for scouts (also auto-explore and auto-pick behaviors).
Enclave Starships went through a bunch of overhauls.
Planets got ship-type preferences to increase planet 'feel' variety (AI Reinforcement Focus).
AIs unlock particular guardians like they do fleet ships, rather than just having access to all of them, increasing variety between games.
Motherfreaking CPA + Exo + Wave synchronization: if a CPA launches, any Exos that are 60% charged will *also* launch at the same time, and any waves that are sufficiently charged will try to launch 90s after the CPA. Oh, and CPAs now launch in carriers.
Roaming Enclaves were revamped to be a smart, coherent fleet that you can give high-level directives to; these guys are like having a friendly player around that can act independently and sensibly enough to be a major asset.
Back in the day, the ships in waves were all the current tech level of the AI; then it was changed so that they gradually transition to the next higher mark to avoid suddenly difficulty spikes in waves.
Various AI mechanics got added at some point, before my time:
* Deepstrike mechanic: if you send ships too deep into AI territory, it spawns threat to discourage such behavior.
* Strategic reserve: the AI has a reserve of strength it can use to spawn ships to defend important worlds that come under attack, especially the homeworlds. Always has spiders, and as of the most recent expansion, it also always has Powerslavers.
* Special Forces: hangs out in AI territory and rushes to defend AI planets that come under attack
* Threat-fleet: freed AI ships that can't find a good way to hit the player will back off into a single coherent fleet and wait for an opening
The energy system got reworked from some horrendously complicated system to 'every planet gets 150k energy' + 'matter converters give 50k energy but -200 metal/s'.
A bunch of minor factions got changed to have intensity sliders instead of just being on/off.
'Helper' player type was added, so you can add a friend mid-game and have them help coordinate ships but not add any extra units to the game (basically an observer that can have shared unit control).
Do you want things that are always-on if you have that expansion enabled? Things like:
Coprocessors, the Superterminal, Core Turret Controllers, Dire Guardian Lairs, Spire Archives, all the 'brutal' core guard posts.