Hmm, the choices are interestingly narrow, in my opinion. I am sure that there are more space 4X games than just that.

A very bizarre list.

SMAC?  Um, whatever.  Great game, to be sure, but 'space based'  Only if you're stretching the taffy from New York to LA.

MoO2 at #1?  I don't really have any rebuttal to that, but meh, I don't think it should be at #1 anymore, seems based more off of the emotional attachment to that game from back when rather than the fact that it's actually 'better' than other contenders who have had decades to improve upon the standard (though for my money MoO is better than 2, but whatever).

My rank of those 5 games would look like this.

1) SotS (because it gets just about everything right, and captures the feel of different races so perfectly)

2) MoO3 (because I'm sick in the head, no seriously, with the user mods/patches that game was so close to perfection for my tastes)

...

everything in a pile somewhere far beneath.

Yes!  Never heard anyone else with that opinion

Wow, seriously?  All I remember is horror (though not as much as my Star Control III horror, of course - what is it with the 3s?).  Maybe I should give it a look again sometime, I might have the original packaging even.

Using the unofficial patches, you get a game that is much better balanced, more stable, and more enjoyable. I wouldn't call it perfect, but it suddenly became fun to play with friends.

That's true of pretty much every "top 5 X games" ever created, pretty much every game review, and almost every thread on this site. This stuff is all subjective. Like putting Sword of the Stars on the list, which I would never do because the UI is terrible and it ruins the game for me. (Or if Sins and SMAC even belong on a "4X" list, which that people can't even agree on exactly what a 4X is demonstrates the point quite nicely.)

"Real analysis" requires objective measurements, and nobody rebuffing the list is using those because you can't objectively measure fun.

I'm confused...

How is the UI in SotS terrible?  Granted, it's your opinion, but I'm curious about why you find it terrible.

The UI in MoO3 was terrible, until it got fixed, and then it was only bad.

I love SMAC, and still play it from time to time.  But it is not, IMHO, a space based 4X game, except in the sense that all 4x games 'happen' in space - even if that space is earth (Civ series) or confined to another planet (SMAC).  Typically, a space based game means interplanetary or higher in scale of game play, along with exploring other planets, solar systems, etc.  Admittedly, I haven't seen one that scales up to actual exploration, between, two or more galaxies.  Porting 'pirates' into space would not make it a space based 4x game.

One game not listed, that is on my list of the top five space based 4x games is: Distant Worlds. I enjoy GalCiv, and SotS (my fav).

I can't get into SotS because of the UI.   Bought the game, tried to play...I just didn't get into it.

I played the SotS demo the other day, and it's a lot more fun than I remembered. I don't like the pace or scale of the game, but I understand why others like it.

The UI isn't bad apart from the research tree, which gives me headaches. (I had to down an ibuprofin at one point.) At the very worst, it's as bad as that of any other space-based 4X TBS. Fleet management is actually handled quite well. 

I realize it's zoomable, but then you have to deal with painfully small icons and poor anti-aliasing. The tree wouldn't have either of these problems if it were represented using projected textures, rather than models. 

I have no problems with the tech tree itself, just how it's represented in the interface. Personally, I like static tech trees more than randomized ones, but different strokes for different folks and all that. 

On another note, I just watched several videos showcasing the interface in SotS II, and it looks fantastic! They've kept the headache-inducing tech tree, but the starmap is excellent! I love the side window with the system view! And everything is nice and flat - no complicated hierarchy of windows like in other games. I'm working on a space-based 4x RTS as a personal project, but have been struggling with the interface. I'll definitely be stealing a lot of these ideas.

I think all the talk about specifics is missing the point. The problem with the tech tree isn't that it's unplayable, it's that it's less playable than its alternatives - namely, the two-dimensional representation used by nearly every other game on the market.

Sure, the problems may not be so bad or maybe they can be ameliorated. But I shouldn't have to settle for not-so-bad or have to do something to ameliorate a problem which need not exist in the first place. (e.g. Yes, the interface can be zoomed, but then technologies are harder to select than they need to be; yes, better aliasing solves some of the problems with resampling, but it doesn't solve all of them; etc.)

Really, I think it comes down to this: interacting with the three-dimensional tech tree just isn't fun enough (for me) to outweigh its disadvantages. Ease of use shouldn't be the only consideration when designed user interfaces - sliders are easy to use, but aren't very fun - but this is a case in which (again, for me) there isn't any advantage to the system, only disadvantages - irrespective of how significant these disadvantages actually are. 

To each their own.

I don't find it any less easy to use than the tech tree in Civ4.

Can you give me an example of a complex and robust tech tree which 'does it right'?  You can't use any of the MoOs, they are neither complex nor robust.  I wouldn't really accept GalCiv either, because if my memory serves me, there was a lot of scrolling to be done there as well.

But I get the feeling that this isn't really a UI issue.  Fun?  Interacting with the tech tree is something you do once every 'X' (where X is usually >8) turns.  The tech pace, as well as the tech design (not the UI) is different from most other 4x games I've played.  In as much as it's not the every turn focus it can be in other games.  I just don't buy this 'the UI is crap' argument, because it's not crap.  It's different, and sure, you may or may not like it, but it's no less inferior to anything else based solely on ease of navigation, or representation of information.  That is, what game gives you that complete tech tree picture which is actually useful?  What game does not require you to scroll (circular vs. flat?  who really cares?) to navigate the tech tree?  Or worse, jump between tabs to see the different areas (more clicky, still have to scroll probably).

So what is the point of UI anyway, if that's really what we're griping about?

Is not a UI issue.  It's a learning curve issue for not just how to use the UI (because come on, the UI in SotS is not difficult to figure out), but what the techs actually are, and how they implemented techs and research as a mechanic in the game.  Or, what do you really want to see?  The whole tech tree laid flat?  That would be rather pointless considering the zoom level you'd have to go out to see the whole thing (as evidenced by those who put it flat on the wiki).

So if you don't like it, so be it, I'm not going to argue that you should like it.  The idea that the UI is bad, is just bizarre to me though, because it does everything you want a UI to do, and it tends to do it with fewer clicks than most other UIs I've seen (you know you can drag it right?).  It also displays the information you need, though sure, you need to do some customizing on zoom level or display setting or whatever, but meh, once you set that up, and once you learn the hot keys it's as fast to get anywhere as anything else, for the level of detail and complexity it contains.

What game does not require you to scroll (circular vs. flat?  who really cares?) to navigate the tech tree? Or worse, jump between tabs to see the different areas (more clicky, still have to scroll probably).

There's nothing wrong with scrolling or tabs. Or at worst, they're necessary evils because of the need to represent a large amount of information on a small screen.
Circular scrolling gives me headaches...