Yeah...the small (on a map) hop across Manila on the EDSA can be a tedious nightmare. If you can, aim to make any Manila transits in the early AM to avoid the worst congestion.
When traveling from Manila (or more South) towards the North Express Way during peak hours, we always try to use the coastal route:
Roxas BVD, Radial Road 10 (past the Pier, Tondo and Smokey Mountain) towards Navotas. Across the Navotas river, take direction 5th Avenue to Caloocan and then finally Bonifacio Av up to the EDSA / North Express Way intersection in Balitawak. This way we completely bypass EDSA.
Admittedly, this route does not exactly bring you through the nicest areas of Manila, but you can easily save an hour compared to the EDSA route during peak hours.
For those of you planning to take the bus up North (usually from Pasay or Cubao), you can take a taxi to Balintawak (EDSA/Express Way intersection) via the coastal route and take a bus there. Otherwise, you will still be stuck on EDSA
But hey, on the bus you can do something relaxing if you are not in a hurry: have some while watching Jackie Chan.