SEIII was the best - it was magnificent on so many levels. Sadly, it doesn't work on 64 bit machines. It's the only game that ever had you build shipyard complexes, rather than relying on the old 'one planet, one ship at a time' thing. You would build stations with variable numbers of docks, and each would work on repairing/building a ship separately. Eventually, as long as you had the resources, a single planet could build hundreds of ships simultaneously. This led to production hubs, supply chains, wars of attrition, constant prioritization and high intensity wars. I still remember slipping cloaked starbusters into pivotal enemy systems, destroying them utterly and then gradually rebuilding the planets individually with mega-engineering devices. There was a ton of variety in ship classes, components, facilities and a slew of combat options (ship classes ranging from tiny ES (escorts) to colossal WS (worldships) and everything in between; carrier warfare; drones; mines; computer viruses; cloaking; electronic warfare; biological warfare etc etc). Vicious fights over wormhole chokepoints until you finally got the technology to open new ones, giving you a massive advantage if you were the first to get said tech.
SEIV is a close runner up and has inherited the throne. Its mod scene was - by far - the best.
I'm not going to talk about SEV. As far as I'm concerned, it doesn't exist. As for non-Malfador games:
- Stellaris could be something very interesting about a year from now, when its systems mature along with its biggest mods
- Endless Space 2 is bland, despite the solid atmosphere/lore; it's too much the child of ES1 and I've got no love for the way it handles combat/war/research
- Star Ruler 1/2 are great, in theory, but only if you have the right mindset, which I don't
- MOO3 with the Tropical/Strawberry mod(s) is a worthy successor to MOO2, despite its reputation. No other space 4X had me mothballing tens of thousands of capital ships, then mobilizing them in waves to fight a war across dozens of systems that would see attrition outpace production. Its scale is truly awesome, despite the lack of SEIII-style flexibility/options
- Stardrive 2 is a decent MOO2 clone (and very self-consciously so); it's more or less competent, if not particularly original
- Stars in Shadow is another MOO2 clone, with a cartoonish art style. It's not bad at all, actually
- Polaris Sector is a wargame masquerading as a 4X title. Also very decent entertainment, even if it outstays its welcome fairly quickly
There are a couple of interesting games in the pipeline:
- Dawn of Andromeda, which is yet another MOO-clone that I still haven't gotten around to playing. Seems bland
- Lords of Rigel is currently in production and slated for a release later in the year. Some original mechanics (like wars between elder races, ala Babylon 5), but more or less the same old ground