I played SC 1, 2 and 3 at the time they came out, and like most people, loved SC 2 to bits but didn't neccessary like the third one that much. Now there are a few things that the last one did well, but at the same time there was a lot that was lost there. I analysed it all a bit and came up with a list of things, that made SC 2 the super great thing it was. So here it is in a form that can be translated to other games of the series if need be.
1) Enigma
SC 2 had alot of things that had a feeling of secrecy and enigma, which just screamed to be unraveled. And not all of them were unraveled in the entire game. A lot of the races had great backstories like the story of mycoon and the hints of Taalo for example were great. Also the Melnorme is a great example of this. Also the whole story of the precursors, Samatra and UrQuans unraveled nicely. There was alot of this in the game! IMO this is something, that SC 3 actually did somewhat well. It also retained the enigmatic feel in the storyline, if not nearly in such a diverse way than in SC 2. This in combination with what SC 3 did not so well though, was...
2) Deranged over-the-top caricaturized humor and diverse races
I mean who comes up with things like the Orz and happy campers? Or Spathi as pathertic fear-driven folks with a ship that looks like something out of a childrens toy box? Or Vux almost vomiting when seeing humans but still talking to them since they want something? 
The races were very diverse and the ones that werent enigmatic, were funny. Or in some cases both. The humor didn't stop at mere jokes, it was on-your-face -type deranged! This was much helped by the fact that...
3) Stylized instead of realism
SC 2 was more like cartoonic, or stylized than realistic. This was probably because of the limits of the graphic stuff at the time, but it worked for their advantage. The biggest drawback in the design of SC 3 was the "realism" they decided to go with when 3D was the boom in the industry. This greatly undermined the possibility for over the top, deranged humor. Think Day of the Tentacle vs. Kings quest VIII. Well, ok, SC 3 wasnt THAT bad, but still. DoTT had a super great style and similar humor, albeit in a very different setting. Something at the very core of SC 2 was lost when going rendered kinda realistic figures.
4) Evolving and epic world with a great storyline
Bringing extinct races back via mating them. Other races going the other way. Kohr Ah annexing their space as the story progresses. Making Chmmr. A lot of huge epic stuff was happening in the game world both storywise and accordingly in game mechanics. This worked for a great immersion from players stand point. Always something new. This is something, that should really be taken into account when allowing users to do worlds - they need robust tools to make epic stories in those worlds aswell! Merely making races with fancy looking ships and planets doesnt cut it.
5) Evolving character
A core game mechanic in RP-style games is the sense of accomplishment and evolvement you get when your stats grow and you get new gear. SC 2 didnt have stats, but it had your ship "gear" getting better and also the management of the fleet you commanded. The latter also had an RP-element in it, since it depended heavily on what choises you made in the storyline. Also, if this game mechanic stops when the main storyline ends, it deteriorates from the playability of user created content. Either find a way to continue it or a reason to reboot the character in the new universes.
and last but not least:
6) Super Melee
Exploration is nice. Gathering resources is nice (as opposed to building buildings in SC3...). But sometimes its good to have some action! The whole SC family did this rather well. What was important was, that it was casual and fun. Not a tight simulation or super strategic, but casual, though it had some light strategic elements to it, like choosing the right ship for combat. You could get good at the specific ship strategies, but they werent that hard to master. Now im all for simulations and all that stuff, but if you think which games work the best (and get played the most) on cellphones, its the casual ones. You could even do a spinoff cellphone game from the super melee to get moar money for the actual game.
What do you think? Got something to add or subtract from the list?
