Horizontal (cost-based) tech tree, generalist factory with the starter one free, smart units have been evoked, and those are the major sticking points IMHO.
Having played Starcraft, AoE2, Warcraft3, Supcom, Dawn of War, Wargame and a few others, I now feel that each of those is a major, unique selling points for Zero-K
The importance and fluidity of map control for resources is also important, and relatively few RTS use it to such an extent. Zero-K is especially notable in how easy it is to raid, take and loose resource points. Other RTS often make taking and defending points a bigger and costlier affair.
Terraform and physics-based combat also helps further setting it apart.
Something else of note is the no-armor/damage-classes, with unit RPS solely determined by their physical characteristics, and the occasional straightforward ability.
This helps each unit make instinctive sense, and it is also what makes having hundreds of different units and structures, each one with its own particularities, manageable in the first place.
The overdrive system is also clever in how it doesn't require micromanagement but opens ways to gain more resources while still keeping map control capital, and requiring strategy. It also degrades gracefully: loosing mex or power plants doesn't suddenly cripple your economy metal makers could, but only degrades it, for example. Unless that was a singu in the middle of your base, but then you chose to make that gamble.
All in all, this plus the effort on powerful UI (the f*cking line move!) makes Zero-K probably the most elegant, and dare I say brilliant RTS I know of. All those elements of design helping reinforce the S in RTS, instead of rote memorization and reflex micromanagement race. Interestingly, it also manages to do that while being a fast-paced game.
(There is room in the videogame landscape for games based on memorization and reflex APM, but those have always been predominant and I much prefer something like Zero-K.)
Other minor details I like about Zero-K: units are robots so when they are a bit stupid and don't mind running to their deaths, it feels slightly less jarring. And the whole style is "cartoony" soft-SF enough to tell you that it's a game, so don't worry if things don't make sense worldbuilding-wise (looking at you Supcom).
Also having only one faction, with factories working as soft-factions without duplicates, is also a clever way to give more tools to the players while still keeping the playstyle variation of factions.
And a great AI that can beat a decent player without cheating or relying (too much) on inhuman micromanagement.
It is interesting to see how all this promote game styles that are rarely seen elsewhere: fast raiding and naked expansion, no storage, or targeting caretakers in priority come to mind.
Seriously, this game has a surprising number of things going for it. I really think it is flat out the best RTS out there, even if it is not necessarily for every RTS player's taste and its presentation lacks the polish an AAA budget could provide.