Jed's mistakes go back way further than Baalke. The pre-Harbaugh regime was also a total disaster. Jed's first coach was Mike Nolan, who ultimately had to be fired after feuding with his #1 draft pick QB Alex Smith (drafted over Aaron Rodgers, remember) over whether Smith was really injured (spoiler alert: he was). Jed fired Nolan and replaced him with Mike Singletary, who was both tactically/strategically incompetent and quickly became a national laughingstock and had to be fired as well.
Building the new stadium is Jed's only real non-Harbaugh accomplishment, but even that has been something of a fiasco. The 49ers are now feuding in court with the city of Santa Clara over accounting for how tax dollars were spent. The stadium was designed without consideration for how the sun would affect spectators, leaving one side of the stadium heavily exposed during the mid-afternoon (it badly needs a roof). The playing surface has been an ongoing disaster that has had to be resodded several times each year. And they managed the new season ticket roll out in such a way as to alienate many of their most loyal, long-term fans (including my father, who had been a season ticket holder for 20+ years at Candlestick but gave up his seats since he would have had to buy a PSL to keep his seats -- at a much higher per ticket price -- in the new stadium).
Jed's done all this in an atmosphere of disdain and secrecy w/r/t the local media, which has created an ongoing PR disaster in which the local reporters are constantly savaging his leadership in the local papers and on twitter.
He also doesn't have Eddie watching over him, by most accounts the two sides of the family don't get along very well. And while his father may be a nice guy, his stewardship of the franchise before turning it over to Jed wasn't much better (nobody fondly remembers the Dennis Ericksen era).
OK, let's start at the beginning here.
First off, both Nolan and Singletary are great examples of "hiring the hot coordinator who everybody thought would be awesome." Nolan was the big ticket coordinator that everyone wanted when they hired him. His dad was a former head coach, he was supposed to be a big deal. Singletary came in without a search as the Nolan hiring was very abrupt, but again, there weren't many voices saying "He won't be able to cut it" when he got the promotion. York hired the guy everyone wanted in Nolan and then he put in the guy that - supposedly - everyone on the defense loved. Giving Nolan GM powers cost them Aaron Rodgers and it also led to structural issues that ran deep. That was a bad move, but when we are making the case that York is a bottom 5 owner.....holy crap, tons of teams make the mistake of hiring "hot coordinator du jour" and then giving him too much power.
As far as the stadium stuff.....to be honest, that is politics. Any city dumb enough to pay for a stadium will get buyer's remorse, but Santa Clara has more money to pay for lawyers than Baltimore does. And he charged PSLs??? Every team in the league has been doing this once they open their new stadium for the last 20+ years! I'm not seeing "bottom 5 owner" on any of this. Neither of those two issues seem wildly unique to York.
Jed York operates in secrecy and disdain for the local media? Frankly....I think that is pretty stupid for an owner to do, but does that really matter in terms of whether he is good, bad or indifferent? Most NFL owners either don't speak to the media or they do so in very limited manners. I do think that a good chunk of the disdain people have for York stems from:
a) His very real, very dumb decision to back Baalke over Harbaugh. I am not letting him off the hook for that one.
b) The fact that the media, who like simple stories of bad people, good people, etc. has decided that they hate the guy. This also happened to Al Davis, who was one of the greatest owners in NFL history.
John York had no interest in running the 49ers. He didn't even want to leave Northeast Ohio. Teams go up and teams go down. Under the Yorks the 49ers won, then lost, then returned to the Super Bowl. That doesn't seem all that bottom 5-esque to me.