The only thing you listed that actually bothers me is the Eagle Vision changes. It now requires you to stand still in order to start it up.
Everything else was easily ignored.
Admit ably a huge chunk of it was disappointments. No real engine improvements, part the notary set back seems to be intended as an anti-hide-and-turn-off-the-TV-for-an-hour to break resources so easily (I owned everything sold by the 3rd section ^_^).
300 bombs really amount to distract with sound/smoke/wtf-ever-coal-does, kill with shrapnel/gas, hell there is a triple inflation to the total number of bombs just by offering changes in the explosion radius. You want to snipe someone in AC, you don't throw a tiny explosive, you shoot them in the face. You want bombs to blow the shit out of a group of them. Functionally, most of the bomb types don't matter either. If you toss from stealth the timed ones work fine and after being seen and chased can be dropped at your feet without blowing you up. Really impact is just for mimicing the old smoke bombs which as still way cooler than, say splashing them with blood since it prevents being shot and lasts longer. Also every time you open the craft menu you are given supplies for three smoke bombs so I mean what's it going to be?
They are tossing more guards at you, probably because you can blow them up now. And the newer handling of hostile takeovers doesn't mean to can sit there and pick everyone off like you could before and it's far far far easier just to run as fast as you can to the guy. In fact, the game really is centered on exploiting bombs, just run up to the guy and drop a couple in the area, bam bam everyone is dead but you.
It's just, to summarize. Last two games were all about giving you bonuses, expanding on things, this one trims back and gives you penalties. Like the Altair sections notably strip you of everything you have or could have obtained. At least Arkham City let us upgrade Catwomen.