...Okay, so I'm not sure the thread title properly represents what I plan on proposing.
Basically, I was playing Fall From Heaven 2 the other day when I realized something: The easiest and most rational way to win in most 4X games is to never attack the strongest opponent, but to instead gobble up as many small opponents as possible until you outstrip every other opponent in all categories of progress. This will generally produce a game that is rife with tedeous, non-straining wars and infrequently large pandemonium, unless the AI starts it first.
A counter weight to this paradox, I think, would be to add a sort of "bully score." A bully score would take effect when a sovereign begins gobbling up numerous smaller opponents by force. The penalty wouldn't take effect unless numerous small opponents were womped, and might diminish as time goes on. "Picking on someone your own size" would incur no bully score.
The actual penalty itself would manifest itself as a broad (and increasing, as the penalty goes up) negative diplomacy modifier for most other opponents, with perhaps the exception of close friends or other bullies. Also, a high bully score will dramatically increase the odds of smaller players forming military alliances with one another against you (perhaps after declaring your third war on a much smaller power, his friends decide that enough is enough!) Each time you are about to declare a war, you might be informed how many bully points you'll pick up, which might flavor your decision.
The point of the bully score isn't to prevent utterly the conquest of significantly smaller opponents, but to make such conquests successively less appealing and large wars against large and medium opponents more appealing. You can see this kind of rationale in real life too--- when Napoleon and Hitler began gobbling up smaller sovereignties, everyone else began getting very nervous.