I can tell you what *wasn't* a problem - the Batmobile. Were there times when it's use was frontloaded for puzzle solving? Sure. The same could be said for every other gadget throughout the series; at least this time around there was a lot to do with it and it added a whole new style of combat and traversal. Was it used a lot in combat? Of course. So is the normal fighting system, and you can bet that after 3 other games in the series, if Rocksteady didn't include a completely new way of engaging with enemies, people would have complained it was just marginal changes - and lets not pretend that having those instances be normal fighting would be so much better. At some point, autocombos and autocounters get old, and that point was starting to show itself by the end of Origins. It was used perhaps more than it should have been, but I maintain that the Batmobile was a necessary addition, and overall I'm glad for it's inclusion.
What was lacking was bits of pieces of everything else. As people have said, there were few truly great boss battles. Coming off of Origins, this was especially weird, since that had the best ones in the series, and you'd think they'd refine what worked so well, but...nope. The boss battles using the Batmobile were appreciated for their variety (that's right), but they needed to do more on top of it. Why didn't they build upon the ideas they had done with Mr. Freeze? Why did Deathstroke end with a tank fight (which was, again, fine, but I wanted more)? Why was the fight with the titular Arkham Knight just a series of predator rooms? Why bring back Scarecrow if he's going to done in so mismatched a manner? This is where the issues with the Batmobile are perhaps more justifiable, but even then, it's not that those sections were bad, per se, it's just that having it be all there was for these villains was just lacking, and added variety would have been appreciated. Really appreciated. Like, a lot.
The level design also seemed to take a step back. I didn't get the sense that the areas were anywhere near as overlapping more multilayered as I remembered other games in the series being. This was also the case in Origins, but compared to Asylum and City? Knight fell flat, again. This one isn't quite as singular,in that I can't so much point to any one area and say "what happened?" but that's because I hardly remember them, unlike my memories of earlier areas from earlier games. It just felt like not even more of the same - it's lesser than what came before. I was Batman, just going from room to room, and I wanted to have to think about things, and explore, instead of just going through linear motions.
Side missions also took a step down. Riddler no longer felt unique and zany, but instead all stuff we had seen before. IIRC, there wasn't even the Hidden Mickey type challenges, which...well, why not? The "lesser baddies" side stuff was all things we had seen before, or, much like the boss battles, included Batmobile stuff which was fine on its own merits but contributed to samey-ness when viewed on a whole. Nothing wrong with Riddler race maps; why was that the end all be all? The body scanning stuff? We saw it in Origins, and it got no more detective-y. Then this is on top of a real "early-mid 2010s Ubisoft" approach to world design: you see an outpost, you clear it out, the map reveals something or other, and nothing happens - repeat 20 times. These could have been interesting if the level design was up to snuff, or if there was more depth to the systems, or if Rocksteady hadn't randomly cut some enemies, but as it stood these all felt really, really, *really* rote.