Just a couple of things off the top of my head:
- Shran, obviously
- Life outside Starfleet, i.e. Horizon. Although we never really got much more elaboration on that aspect
- Shuttlepods before transporters (early on at least)
- MACOs - implying that Starfleet hadn't adopted a particularly militaristic attitude at this point and specially trained people needed to be brought in.
- Spatial torpedoes, hull plating and plasma cannons. It's retro enough

- Alien languages being a problem
- A darker atmosphere for season 3 than even DS9 gave us at times
- I think it goes without saying that season 4 was full of little gems and references to the previous series
- Vulcan attitudes evolving. I have to admit, I loved the idea of them being superior and arrogant early on and causing friction with humans at times.
- Archer not being bound by the Prime Directive and occasionally doing stuff that we know none of the other captains would do (even Kirk

)
- Section 31
- Oh and this: "A
POOP question, sir?!" Finally addressing what we'd all been asking for nearly 40 years
