When I first started playing TF, I was plagued by main connections, but then at the end of January, a patch came out that fixed a main connection bug and all of a sudden, I find building bypasses solves the problem 99% of the time (the other 1% can be solved with a more elaborate bypass).
@Shades: Have you updated your TF build to the latest version? Are any of the country roads going in to your city main connections? If you can find two such roads, make sure there’s an alternative connection between these roads that bypasses the city altogether.