I've seen the finale. S5 was very inconsistent when it came to continuity and animation so I didn't give it much thought that Magneto was more villainized here. He's a lot more neutral in earlier seasons. I don't have a problem with Scott's issue with Magneto but I do think he's way too hard on Xavier and I don't remember Jean ever calling out Xavier. It seemed Scott was the only one with issues besides Rogue, which demonstrates Scott's own insecurities. I haven't found him very sympathetic and it's a bit hypocritical of him to get angry at Xavier for turning his back on the X-Men when he did the same thing to Jean after the Maddie incident. Beau has written Jean to be very patient and understanding here because I feel Jean should have been allowed to vent more and call out Scott for his actions. In X-Factor, Jean was allowed to be angry about how her life was taken away from her and that while she wasn't the only victim, she was still a victim. In fact, of everyone involved, Jean is the biggest victim because she's the catalyst for everything that went wrong with her kidnapping/replacement.
And back to Magneto, Scott is aware of how close Xavier and Magneto are so despite his own personal issues, it's selfish and presumptuous of him to feel the X-Men and everything Xavier owned should be bequeathed to him. Magneto is Xavier's friend so Xavier has every right to designate him the mansion.