I think the problem are the rose-tinted glasses. People don't just want MoO2: The Space Empire Boardgame Ruleset in Machine Code, they want the feels of playing that game for the first time when they were 12, when everything it did was still fresh and innovative (though, in part, copypasted straight from their own MoM). The developers, being practical engineer types, don't seem to grasp that there is no way for them to recapture those feelings with a piece of software that replicates the functionality of MoO. You have to make something new that will feel equally fresh, today.
I mean, I admit that Civ 5 may be a good game. But I'm not going to play it; I remember the time when I was 9, and Civ 1 (never got 2) blew my mind because I didn't realize "this is a thing a computer can do." The modern Civ may well be superior to it in every way, but now I have points of reference like CK2 that kill any desire to get into the new Civ.
Will I understand this if I have never played any Masters of Orion?
You really should. There's a reason everyone has been copying those damn things for 20 years. Though, surprisingly, no many people, except the makers of Age of Wonders, have tried to copy Master of Magic, which was the real progenitor of MoO2 and the superior game. A game that shows how to properly succeed a classic is Dominions (1-4), which can be seen as a spiritual successor of MoM.
Not sure if you listened to the podcast but Paul takes pretty much this perspective - he argues that the uniqueness of the universe/races hasn't really been replicated since MoO2. He's a MoO fanboy, Rob isn't. Both of them don't seem to be big fans of really any 4X games since then.
I don't think there's much use in replicating anything in MoO. In retrospect, all the races and the "world building," for what it was worth, were pure cheese. You can't replicate it without making a parody.
I think the same thing happened with Alpha Centauri. All the attempts to replicate it have been but pale shadows because the real meat of what made Alpha Centauri great was the setting and the writing - the 4X mechanics were pretty standard, with some innovation but not enough to solely explain why it's so beloved.
Alpha Centauri is slightly different, because the only innovative thing about it
was the fluff. It created an artificial atmosphere by practically forcing the fluff down your throat, but years later it's just way too transparent a re-skin of Civ.
The thing that annoys / worries me is that a substantial number of commentators these days seem to take the position that SMAC wasn't really that good and its fervent support comes from achieving a critical mass of nostalgia goggles + bandwaggoning, which leads to a positive feedback loop of rabid fanboyism.
I mean, on the surface that seems to me patently absurd, but then again that's exactly what I would say if I were indeed brain-infected with a critical mass of nostalgia goggles + bandwaggoning. :/
I dare you to go and try it, right now. It hasn't aged well - just usual 4X tedium dressed in pretentious technobabble. Master of Magic, on the other hand, is perfectly playable (and, arguably, has a better UI...).