Mostly because, due to team's mutual consent, only modern flags are used (even for Incas!). We could one day make alternate flag scheme, though. Then, Kalmar Union flag for Scandinavia is a sure bet - I'd probably like to see it myself.
Still, "Scandinavia" civ mostly resembles Sweden (and all the rest of Scandinavia, except for Denmark, has been for some time ruled by Sweden) - so Swedish flag is more or less appropriate. Then again, I guess the same thing can be said about Denmark too.