They just need to make surrenders a part of the diplomacy system. Essentially surrenders should put the civ's planets into a quasi-owned state. Something like (the following is just a rough idea):
1. Make it so that surrenders can be refused. Accepting the surrender from a culture you are not at war with will lessen relations with the races that were at war with them.
2. Flag all the worlds as "surrendering" for 5-10 turns (or whatever) after the surrender happens in any case.
3. You can negotiate with the AI your enemy surrendered to. If you are on good terms, then they'll give you control of those worlds. If you are enemies then they'll say "bite me," or the equivalent. A.I.'s might be more inclined to keep planets that are well in their cultural influence however.
4. Taking worlds that are flagged as "surrendering" is easier (combat bonus down), but is grounds for war (but the AI can choose not to go to war if they don't think it is a good idea).
5. Sometimes minor races can spawn from surrendering worlds, the minor race the world becomes should usually have a different personality than the original race. They're still flagged as surrendering for the standard duration.
6. Even after a surrender is over, those worlds remain more vulnerable to flipping sides due to influence than normal worlds for some period of time.
7. (Someday): A Civ can surrender to more than one race, in which case they negotiate how to divide up the planets (and potentially have to fight off other combatants who were in the war).
Of course, the AI can surrender a bit too easily and this needs to be fixed. Also, other AIs should perhaps be more inclined to intervene in wars. One problem is that the AI will tend to NEVER go to war with the strongest guy or any guy a lot stronger than them. This is bad when they could potentially have overwhelming forces by joining up with another few Civs that are already at war with them--and the AI should also look at how likely it is that it could get others to war on such a civ. Of course, evil Civs are more likely to gang up on good civs and be otherwise opportunistic; good Civs are less likely to help evil Civs and more likely to go to war against evil civs or to help another good Civ. Neutral Civs would be somewhere inbetween (and hence largely self-interested with a good bit of loyalty to friends thrown in).
There is some of this in the game already, but I don't think quite enough. I know in one game I was taking out a major power and I couldn't get anyone to help me do it, nor did they ever stop me even when it was clear I was gaining overwhelming power (and would gain a ton of influence to boot). The AI should watch for things like that.