why are regional cruising altitudes higher than those of international much longer flights? How come, for example, the average cruising altitude of let's say the Westjet Boeing 737-600 from CYWG to CYVR flies at an altitude of 38,000 feet-40,000 feet, yet the Air Transat Airbus 330-200 flying from CYVR to Man EGCC flies between 33,000 feet and 35,000 feet?
Why is the air transat one flies lower when you'd think that with the Vancouver to Manchester route being more of a long-range flight than the Winnipeg to Vancouver one, it'd want to fly above the regional/domestic flights.

Why is this so?
to illustrate, here are flightaware records for two recent flights: 
Westjet: https://flightaware.com/live/flight/WJA307/history/20150903/1210Z/CYWG/CYVR
Air Transat: http://flightaware.com/live/flight/TSC284
Flight altitudes have relatively little to do with whether a flight is regional or international per se. More important factors include the winds aloft and the individual aircraft capability.

In the case of the Winnipeg to Manchester flight, they were probably using the North Atlantic Track System (NATS). The winds aloft over the North Atlantic are generally out of the west. The routes of the tracks are arranged each day to take advantage of the those winds. The track system puts the eastbound aircraft on tracks and at altitudes that would maximize the tailwinds, and westbound aircraft on tracks and at altitudes that minimize the headwind.

Since the winds aloft in the northern hemisphere are more often than not westerly, the Winnipeg to Vancouver flight might well have been fighting a headwind, but the strongest winds aloft tend to occur in the mid 30s, which can mean that you can lessen the headwind by climbing higher.

Aircraft capability also plays a major role, and aircraft vary widely in what they can do altitude wise. For example, a 747-200 up against its max takeoff weight of 800,000+ lbs can initially climb to only about 31,000 feet (FL310), but towards the end of the flight can reach FL390 and above.