Well, this is a bit surprising.

Sources: Alex Anthopoulos leaving #BlueJays after turning down extension: https://t.co/XgO8q7D1J3

— Shi Davidi (@ShiDavidi) October 29, 2015

Sources: #BlueJays offered Anthopoulos long-term contract. His departure is not over terms or money.

— Ken Rosenthal (@Ken_Rosenthal) October 29, 2015

Alex Anthopoulos wanted full GM responsibilities. He told me recently he wouldn't stay under conditions less than that.

— steve simmons (@simmonssteve) October 29, 2015

Source: In their 1st & only meeting, new Jays prez Mark Shapiro scolded Alex Anthopolous & staff for trading so many top prospects this yr

— Rick Westhead (@rwesthead) October 29, 2015

The Blue Jays have been publicly looking for a baseball guy to replace Paul Beeston as team president for over a year, beginning with their awkward courtship of Kenny Williams and Dan Duquette last winter. They finally found their replacement in August, when they brought Mark Shapiro over from Cleveland to take the job, though the announcement at the time suggested that Shapiro would focus mostly on the business side of the organization, leaving the baseball operations department in Anthopoulos’ hands. After the team won the AL East on the backs of his many acquisitions over the last year, the general assumption was that he’d done enough to earn autonomy as the guy putting together the team’s roster.

But perhaps we should have seen this coming, given that the organization was clearly looking for a former GM to take their presidents role, rather than focusing solely on someone with a business background. They made a point of hiring a baseball guy to be Anthopoulos’ new boss, and it’s probably difficult to assume that you’re going to be allowed to make decisions if your boss was hired in large part because he’d done your job before.

So now a great 2015 Blue Jays season ends with a stain, as the team will have to undergo changes in the baseball operations department as well. Shapiro’s lengthy tenure in Cleveland helped produce many front office members around the game and the team’s position should help attract quality candidates; I’d suggest this might be the kind of job that could get Ben Cherington to reconsider taking a year off from working in baseball, for instance.

But this is an awkward cap to put on a great year in Toronto. Anthopoulos absolutely did trade away huge chunks of the team’s farm system, but in acquiring guys like Josh Donaldson, Troy Tulowitzki, Devon Travis, and Russell Martin, he made moves that set the team up to win not just in 2015, but beyond as well. And focusing solely on the cost of the acquisitions without balancing that against the obvious rewards of reinvigorating a city that hadn’t seen playoff baseball in 20 years seems short-sighted at best.

The Blue Jays will probably be fine without Anthopoulos, but the Jays are going to have to do some pretty nifty PR to not squander the significant excitement for the franchise they just spent so much time generating. And while there aren’t any other GM jobs open at the moment, it seems pretty likely that Anthopoulos will find a job in the not too distant future, and probably one where he’s allowed to call his own shots, rather than reporting to a GM-turned-president who doesn’t share his same philosophies.