Sorry bud, I might not have put that well. When I said Whitecaps Prospects was probably scrapped, I didn't mean that Vancouver's academy was - rather that one of their many development teams, specifically the one named "Vancouver Whitecaps Prospects", has likely been dis-established. The Under-23 team (Vancouver Whitecaps Residency) still exists, and it is this team for which McKendry is attached to rather than the defunct Vancouver Whitecaps Prospect team you linked to earlier (although you're hardly to blame for Wikipedia being inaccurate ). Toronto FC has one academy team. Vancouver Whitecaps FC has several, and is regarded as having the best developmental system in all of Canada.
Vancouver has programs all the way down to Under-12 level for both genders, and were heavy pushers for the recent MLS development reform that allows for greater room to promote academy players. The Whitecaps will certainly retain this developmental focus in MLS. Hopefully (as a supporter of both Canadian and Kiwi football, and a long-time Whitecaps follower) McKendry will get a decent go in the Whitecaps system.