Most 4x games share a fatal flaw -- endgame slowdown. Everyone who's played civilization has experienced this issue: at the start of the game your turns take 5 seconds, and by the end of the game you're spending 3 to 4 minutes per turn. This starts to significantly delay the positive feedback that you get from making good decisions, forcing you to make a decision (I'm going to attack Catherine), and then only see the result an hour later.
Some games have no mechanisms to combat this issue, but Civilization 5 came up with an interesting solution, by giving special benefits to small empires. These small empires (1 - 4 cities or so) get to advance along an alternate tech tree at a faster pace than larger empires do. Additionally, when conquering an enemy city you can choose to incorporate it fully into your empire, or turn it into a puppet state. Puppet states still provide you with resources, but are uncontrollable and don't count towards your total number of cities. In this way, a player can continue to only manage a handful of cities all game, all while building, conquering, negotiating with other leaders, etc. Since they released Civ 5, I haven't been able to play through one game with a large empire. I've tried, but every time I give up after a few hundred turns and start a new game with a small empire. I don't think I'll ever go back.
For Deep Field, I wanted to have a mechanic that similarly reduced the amount of endgame slowdown. I decided to incorporate a 'mothership' token, which essentially forces the player to only take action at a specific location. If they want to colonize a new star system, they have to move there and colonize it themselves. If they want to build buildings, they have to fly to the system and queue the buildings up. If they want to attack an enemy star system, they have to transfer some of their fleet to their mothership, fly to the system, and initiate the fight. This system means that a turn takes the same amount of time during all periods of the game.
The mothership also had additional effects on the flow of the game -- at the start of a game you spend most of your time colonizing, building, and exploring. By the end of the game, most of your time is spent fighting enemies and conquering planets. Additionally, it forces interesting strategic choices and encourages players to play by feel rather than working out the perfect set of moves for any particular situation. I feel that overall the mothership mechanic has been a big success.
4x Lesson Learned
Endgame slowdown is something to try and avoid. No one wants to spend 10 times as long to see the result of their decisions at the end of the game compared to the beginning.