Just caught up in that most recent speculation - and I thought exactly the same thing (and wrote it down in my review in my blog the day after I watched the movie *lol*). Why should Blake make the connection, and nobody else? What's so special about him to see beyond everything in a way no one else does?
Honestly, the movies really don't reflect well on Gordon's abilities as a cop, especially when supercop Blake puts things together in one step instead of the multiple hints Gordon was given.
Gordon doesn't have Blake's little orphan insight into Bruce's/Batman's psyche, but he does know Bruce Wayne was orphaned as a young boy and that he comforted him at the station, so it would make sense for Wayne to build on that connection later in life by teaming with Gordon again and for him to be motivated to fight crime based on his childhood trauma.
He knows Bruce's parents were murdered by a man who was murdered by Carmine Falcone, the first crime boss Batman went after.
He knows Bruce disappeared right after the Joe Chill shooting and reappeared years later at the same time Batman first started fighting crime.
He knows Bruce heavily supported Harvey Dent and held fundraisers for him, and that Batman shared his respect for Dent.
He knows Bruce saved Coleman Reese's life (the man who was about to reveal Batman's identity). All you'd have to do was check who Reese worked for as an accountant (Wayne Enterprises) or just ask him some questions. At that point Reese didn't want to give up Bruce's name and Gordon doesn't want to out him, but just for curiosity's sake, you'd think he'd follow up. Plus, even with all the chaos following the Joker's terrorism, did no other cops follow up on this; not even Matthew Modine? I guess Gordon suppressed the investigation, which would look suspicious in and of itself.
He knows that Bruce disappeared into a secret chamber in his penthouse a minute before Batman showed up without any apparent entry, he knows that Batman dove out a window to save the daughter of Bruce Wayne's former housekeeper and someone who the press would see he was close to, and he knows that Batman called her "Rachel" by name and raced to save her instead of Harvey Dent, not knowing that Joker had pulled a switcheroo.
He knows that Batman stopped operating at the same time Bruce Wayne became a crippled recluse.
He knows that all those gadgets and vehicles would have to come from a company with military contracts and that Batman would have to be someone wealthy with lots of free time on his hands.
He knows that the Tumbler and the Bat-Pod were always heading in a certain direction when the police lost track of them (first toward Wayne Manor, and later toward the Wayne Enterprises lot at the Gotham docks).
Gordon's no Columbo, that's for sure. And that's before I add on the fact that he sent almost the entire Gotham police force into an underground trap, that he sent the only two DAs working on the largest case against the mob home with the two cops he had been told before by Dent were working for the mob themselves, that he partnered with someone who was a mob enforcer that he saw getting paid off right in front of him (yeah, he excused it by saying if he didn't work with corrupt cops he'd work alone, but that's pretty bad), and that he participated in a coverup and conspiracy. Harvey had every right to be pissed at him, even if he went about it in the completely wrong way (and Harvey wasn't a great guy even before going crazy either consider he was willing to torture to get a confession). Gordon's not a good cop in either ethics or ability, it's just that everyone else was so lousy he floated above the rest of the riffraff.