I wouldn't say that the leaders expansion constitutes a "normal" game every gaming group is going to play the game differently.
Here is a breakdown of all the variants we have played with and our feeling on them.
The Long War: Have not tried this variant yet.
Age of Empire: Have not tried this variant yet.
Distant Suns: we often do not play with as it can dramatically slow the early game down as well as making the game even more random and giving some players that hit good tokens a significant edge which in the early game can really have a big impact further down the road.
Leaders: If your group is experienced with the game and has been playing with leaders a long time than it may just come naturally and add a little bit of flavor. Our group tends to have new players cycling in fairly often so it is an option that adds a whole lot of rules to remember and really doesn't add all that much to the game. The capturing leaders aspect is really neat but happens rarely and when it does, often they are not as powerful of a bargaining chip as one would expect.
Sabotage Runs: Have not tried this option yet. Looks cool but seems like it is often a waste of fighters as the odds of succeeding are very slim.
Imperial II: Have not tried this variant yet.
Variant Strategy Cards: Our groups standard game is played with the following cards - Leadership, Diplomacy II, Assembly II, Production, Trade II, Warfare, Technology II, Bureaucracy.
Variant Objectives: We include the extra objectives, more variables make each game different.
Race Specific Technologies: Always included, this is one of the best options that either expansion brings.
Artifacts: Speeds up the game a bit and usually causes more intense fights over systems other than Mecatol Rex
Shock Troops: Have not tried this variant yet.
Space Mines: Have not tried this variant yet.
Wormhole Nexus: We include this system in most games, it makes the wormholes always in play if you have randomly selected the tiles with which to build the galaxy and lets players that may not have any interaction have a chance to strike to the far reaches of space.
Facilities: Another easy factor that can speed the game up a little bit although they are more effective for races with easy access to trade goods.
Tactical Retreats: We enjoy this variant, although some people may say that it makes the game less strategic and makes CC a little less valuable, we find it is slightly more realistic than having a fleet trapped in a losing fight.
Territorial Distant Suns: Have not tried this yet but may do so soon, looks much more balanced than the old Distant Suns
Custodians of Mecatol Rex: Have not tried this variant yet.
Voice of the Council: Have not tried this variant yet.
Simulated Early Turns: Have not tried this variant yet. Probably won't try it, our early turns are pretty fast already.
Shards of the Throne
Preliminary Objectives: Speed up the game, but not enough of them to make each game unique so often it is easy to see which one each player is going for. Despite that, they are a staple in our group, anything that speeds the game tends to be.
Flagships: Very cool, minimal extra rules for people to grasp, the only downside is that a few races have extremely powerful flagships compared to others.
The Final Frontier: Have not tried this variant yet.
Mechanized Units: Who doesn't want to play a game with tanks in it. Always included for us, easy to add to any game.
Mercenaries: Have not tried this variant yet, but it is next on our list.
Political Intrigue: The Political Intrigue option has been our groups favorite. It gives some added excitement to the political part of the game without too many extra rules.
Fall of the Empire: Have not tried this variant yet.
So that is our breakdown. I would say of all the options the top ones would be the new Strategy Cards, Political Intrigue, Race Specific Tech, and Tactical Retreats. Leaders are cool but like I said they can be a lot to handle for newer players, Flagships are very fun but can be unbalanced. Preliminary Objectives, Facilities, Artifacts, and the Wormhole Nexus are all nice quality of life additions.
Distant Suns is the only one we avoid but it may be better with the Territorial option.
There are a lot of options and that keeps the game fresh, we are looking forward to seeing how Mercenaries play out next game.
I hope you have fun building your groups personal set of variants that will make the game unique and exciting for you.