Ok, so here we go:
First of all, I will preface this by saying I did not care for Clone Wars at all, so that has a huge impact on my views of season 2. In total, there was probably 10 episodes of CW that I genuinely liked. During the first season and the introduction-2-episode-movie of the second season of Rebels, I was seeing some old school Star Wars magic. I thought Dave Filoni had put in more substance than he had during CW. To me, CW was a very cheap brand of entertainment, and he did a lot of things just for flavor.
In season two of Rebels, it was like Dave went back to his toy box and just started pulling out nostalgia items and cramming them into Rebels, whether they fit or not. The old clones, Ashoka, and Darth Maul were the biggest issues I had. It was like he just can't let go of those characters so he has to figure out a way to fit them in, and he essentially said as much during one of their panels last year. I can handle Ashoka being in it if they want to do a little "last known surviving Jedi" storyline, but using her as a focal point throughout the season made it seem really cheap. I think Filoni learned a bit too much from GL, and like the prequels, sacrifices impactful substance for flavor.
Secondly, there are no extended themes or arcs in this show. I think they need to put more faith in today's children- that they can focus on a story that lasts for more than 22 minutes. The one off format doesn't provide enough time to develop the characters and relationships, so you end up with a character that is essentially the same from beginning of the series to the end. Ezra had a little bit of development throughout season 2, but the rest of the characters are essentially the same as they were in s1e1.
Elements that I didn't care for were the Mandalorian pilots, but that is completely personal. I could go on a rant about how the CW destroyed Mandalorians, but for now I'll just say... I don't like what the Mandalorians are in canon. The space whales were really really really stupid. That was taking concept art and hamfistedly smashing it into a show... because why? Because it was concept art once? The go-go-gadget-sabercopters were an absolute atrocity. Like I was saying before, it was something done completely in the name of style, foregoing any decent concept or substance. Another style over substance thing was Vader surfing on his fighter, for what reason other than Dave Filoni was playing with his Darth Vader action figure and thought it would be "totally badass" if Darth Vader was "just like totally standing on top of his fighter as he drifted into battle because that is totally ominous" would that exist? THAT IS CANON NOW! Darth Vader force-surfs on his TIE fighter.
And lastly, DARTH MAUL! Dave... let him go already, dude! He died in TPM and he never really had a personality or character traits to begin with. He was a lightsaber ballerina, and that's all he was ever supposed to be. Now, we have Maul die and come back and die and come back and die and come back, and die again... maybe? The CW made the robot-spider-legs Darth Maul arc stupid, and now Rebels just keeps slamming his stupid horned-head down our throats.
There were a handful of smaller elements that I didn't care for, but those were the big ones that rubbed me the wrong way throughout the season. It just started to lose it's ties to SW, and became some generic adventure show. Especially, that last episode. The last episode felt like some dungeon crawler movie... not Star Wars. In summation, I like to go to a galaxy far, far away, and it just didn't take me there.