The criticism around Clara is an extension of the criticism that’s existed since the start of the reboot: that the companions get too much focus. Rose was very much the entry angle to the revival and made sense but the argument goes that Clara took that too far. She feels like the main protagonist in a lot of stories and her departure is a little controversial in that vein but I’ll avoid spoiling that.
replyThe nullified thing is known as the “timeless child” storyline. The Doctor is retconned to not be a Gallifreyan at all and also the source of everyone’s regenerative powers (or something, I honestly forget). It was a totally unnecessary retcon but IMO much worse it was incredibly self indulgent. Most of the audience cares very little about the Doctor’s backstory, they just want enough setup to enjoy the adventures.