[Edit] The purpose of a national highway system is to connect cities, not avoid them. I'd get rid of the GB\CO routes too, but I'd replace it with a route through Toronto by via 400/401.
Better yet, why not implement a general national highway system and scrap the strictly transcontinental "Trans-Canada" Highway? That would make more sense. The TCH as-is has a lot of branches that piggyback over middle-of-nowhere roads that in themselves go nowhere, while important routes are not part of it.
I've proposed this a couple times as well. Model it after the German model, where routes 1-9 are primary "national" routes, with 11-99 being primary provincial routes, and 100-999 being spur and regional routes. Basically, you'd wind up with this:
Route 1: BC Hwy 1, AB Hwy 1, SK Hwy 1, MB Hwy 1, ON Hwy 17/417, QC Aut 40, QC Aut 30 (Montreal By-pass), QC Aut 20, QC Aut/Rte 85/185, NB Rte 2, NS Hwy 104, NS 105, NL Hwy 1
Route 2: BC Hwy 99, BC Hwy 97, YK Hwy 1 (Alaska Highway)
Route 3: ON Hwy 401, QC Aut 20, QC Aut 10 (potential future connection to a northern Maine interstate for a faster connection to southern Atlantic Canada)
Route 4: AB Hwy 4, AB Hwy 3, AB Hwy 2, AB Hwy 35, NWT Hwy 1, NWT Hwy 3
Route 5: NB Rte 1, NB Rte 2, NB Rte 15, NB Rte 16, PEI Rte 1, NS Route 106
Route 6: ON QEW, ON Hwy 427, ON Hwy 401, ON Hwy 400
Route 7: QC Aut 40, QC Rte 138 (plus gaps filled in), NL Hwy 430
Route 8: QC Aut 15, QC Rte 117, ON Hwy 11
Route 9: BC Hwy 16, AB Hwy 16, SK Hwy 16, MB Hwy 16
As for the Provincial routes, BC would get numbers 10-19, AB 19-29, SK 30-39, MB 40-49, ON 50-69, QC 70-89, and Atlantic Canada 90-99, with routes ending in 0 or 5 being main non-national routes (just like US interstates).