I like Evil Muppet's mega event suggestion, which I will expand on.
For another, how about reviving all of the races that have been previously wiped out (maybe through some kind of time travel event). Give them each one of the class 0 worlds (which of course have been upgraded to class 26). - Or, perhaps alternatively, use a spare civilization slot to spawn a custom opponent from the player's collection. Give them a small empire by upgrading all of the class 0 worlds in one system to class 10."]

For another, how about reviving all of the races that have been previously wiped out (maybe through some kind of time travel event). Give them each one of the class 0 worlds (which of course have been upgraded to class 26). - Or, perhaps alternatively, use a spare civilization slot to spawn a custom opponent from the player's collection. Give them a small empire by upgrading all of the class 0 worlds in one system to class 10.
Instead of having it be a 'time travel event', how about it be a rebellion? This would mainly affect evil civs more than good or neutral ones (though those can experience this as well). These civs wouldn't come back and be their old selfs, they'd be different. For example, the Altarian Republic. Say they're conquered by the Drengin. Months or years after this they manage to overthrow the Drengin. They wouldn't necessarily get their homeworld back but they would gain like say 5 worlds, all of which would be worlds they had originally in their Republic. These worlds would be in the same sector and they would have Drengin ships which they 'acquired' and would have the Altarian colors on them. The name of the new Altarian government would be different and it would also be a different ethical alignment, like Altarian Empire, Altarian Alliance, Altarian Federation, Altarian Union, Altarian Dynasty, Altarian Imperium, ect. and the name would coincide with the ethical alignment, Empire, and Imperium would be evil for instance.
Another thing would that would be nice to see is when worlds breakaway from your civ and for the Independent League (or some other civ), the person you see in the diplomacy screen should be of your race. Right now, different race portraits come up. If you haven't conquered a Minor civ, the portrait should be of someone that is a Terran or Drengin.
Minor powers need to be more aggressive than they are. They should build warships and troop transports more than building a massive number of constructors for starbases that are pointless to them. Give them the ability to wage war effectively and once they obtain a certain number of planets they would then become a major power.