I dont think its too helpful to think of them as completely different comics (I still just call it all HS2), and also the comic was shut down for years due to the extreme levels of harassment directed at the first team (harassment which big swaths of reddit et al accused Hussie of lying about (seriously)), so I've never been much inclined to focus on the negatives here.
All that said... I do have some problems. Some of these are associated with the inadvisety of attempting to write a sequel to the Epilogues in the first place. Even though Meat obviously sets up a sequel hook, and the two "books" are deeply intertwined, I strongly feel that Candy is a perfect ending to Homestuck. And many of the interesting places it ends off on are immediately reversed by HS2 in a way that suggests someone did not even understand these decisions were being made. It's baffling to me.