I think they should make the surrender a bit more interesting than just "here's our stuff". A nice solution would be to make the surrendering civilization a vassal to your empire. "We surrender. Spare us. We submit to your rule." This could be implemented with the existing game mechanics so you wouldn't need to add that much new code to the game:
- If the capitulating civilization is a major one it's status is "conquered". This way the surrender counts towards a conquest victory.
- From now on it's considered a permanent ally to you regardless whether you have the tech for this diplomatic option or not. When you go to war, it goes to war with you. It won't break the alliance, either, no matter what you do. It's a conquered nation. This way the surrender counts towards a diplomatic victory.
- The vassal's influence is added to yours, thus counting towards an influence victory.
- The output of the vassal's ascension crystals go to you from this point onwards helping you towards an ascension victory.
- You and your vassal have automatic open borders, exploration, non-aggression, cultural, and free-trade treaties. You get all resources the vassal isn't currently using and any new ones it happens to get. You automatically share technological discoveries (or alternatively pour your research together). This will help you towards a technology victory.
- The surrendered civilization keeps its remaining planets and continues to administer them. Same with its ships and other stuff. This way you won't have to bother with destroying them or micromanaging its territory.
- To the rest of the galaxy, the vassal state is seen as part of your empire. They will attack it only if they want to attack you and the decision calculations include both of you and your vassal combined. The vassal has no independent foreign policy, either. If the others are mad to you they are mad to your vassal, too. If they like you, they like the vassal.
- In the UP the vassal votes with you.
Traditionally empires were built with many different parts. Having vassals as part of your empire would make it interesting and open up new ways to play the game. And all the mechanics is already there. It just needs to be combined into a "surrender package".