Moremiles:
Customs is an issue. Only a small handful of flights to the US are not pre-cleared--those are the flights from smaller centres (e.g. YHZ, YSJ, YYJ and YQB) and the flights from third country carriers who don't pay for pre-clearance, (e.g. CX YVR-JFK).
The vast majority of flights leave from the pre-cleared stations. You cannot mix passengers in sterile transit with US bound passengers on a pre-cleared flight--so either the entire flight is sterile, making it useless for US bound passengers, or you require transit passengers to pre-clear.
As for why we allow the Americans to operate pre-flight inspection--we do it for the same reason the the Bermudians, the Irish and the Bahamians do. The Americans want to do it, and the airlines are prepared to pay for it.
Canadian passengers would not have access to most of the smaller airports that AC and the US carriers fly to (not to mention a couple of majors like LGA and DCA) were it not for the fact that these flights are pre-cleared.
While the Americans would certainly allow for reciprocal pre-clearance stations (it is in the Agreement), it is not really attractive to us--there are too many US points of departure, coming to relatively few Canadian airports. The cost of assigning Canadian officers to these points is high, and airlines are not overly keen to provide the real estate.
Looking into my crystal ball, however, I would be prepared to wager that the next pre-flight inspection station may well be a joint Canada-US station, located in a third country. A pilot project could be set up in BDA very quickly to test joint operations and information sharing.
For full implementation the obvious candidate is LHR. You could easily sterilize the far pier of T3--after all, AA and UA pretty much own it. The UK government would be reasonably likely to cooperate on such an arrangement--provided that they can get their house in order on réfoulement.