Well, you assume here that the master and the colony will work together, which is not the case at all. In my last game, it only took about 50 turns for one of the colonies to become independent (and henceforth be hated by the former master). Also, even if they stick together, they don't actually combine their military force, therefore they are weaker by definition and less likely to stand up to you. As far as I know they don't share resources (as in "having one resource is enough for both of them"). And so on... if you think two separate AIs are the same as one bigger one, you are very mistaken.
I've never seen colonies declare war on their masters. You're right, vassal+master isn't as good as if it was a "permanent alliance" where they can share resources and stuff.
But is it really a bad bug? I'm not sure when the AI decides to break off the colony, but is it when the "Sid tips" nags the player to do it? I was playing a game when I got the nag to create a 5-city colony, so I tested how much I'd lose by doing it.
I saved $100 in expenses, but lost $400 in revenue (taxes set at 100% wealth), for a net loss of $300 per turn. (If my taxes were 100% research, I'd be down about 400 beakers but up 100 coins.)
It just didn't seem like a big deal. I was down about 25% in income overall, but got a friendly vassal in return. As a human player, that vassal is kind of useless because I can't control it. But doesn't the computer AI do a better job at that?
I don't think of creating a colony as a win-win scenario. It's more like a "dump these cities because I can't be bothered managing them anymore". A friendly vassal seems like a decent tradeoff for less micro-managing. I lose some income, but (if the vassal is smart, which admittingly he often isn't), we still have the same combined hammers and more combined income. Two computer allies may be able to make use of those combined hammers and income more effectively than a human master + AI vassal.
What about if you have permanent alliances turned on? Can a vassal and master form a permanent alliance? That would seem to allow the full benefits of resources and tech research, in addition to removing the colony expenses. Anyone ever seen this in a game?
Okay, I do agree the computer does create colonies too easily. However, I wouldn't want to see them
never create colonies if that was "fixed" in a patch.