I have no idea what the problem was. Players not interested in coming here? An unwillingness to step outside of their valuations? A weird confidence in the players they currently have? It's probably a lot of factors, but all I actually know is that they've failed to this point, and that sucks.
The problem I have with your analysis is that it's 100% just made up in your head. Like... there's absolutely zero evidence that the Jays just sat around waiting on Soto and didn't do anything while they waited, or that the Yankees laid tons of groundwork to be able to move on. Knowing the Jays MO of being interested in everyone, the most likely scenario is that they did lay tons of groundwork all g the way and have just failed to close deals.
The Jays being runner up to others has become a meme the last two years. If they weren't prepared to move on to their next target, they wouldn't be one of the finalists for every player who signs.