One of the things in the Donner movies I've never liked is the depowering and having sex with Lois. Singer grabbed ahold of this idea and extrapolated what would happen if Lois got pregnant from that union. He's connecting himself to the Donenrverse in this way, but the rest of his behavior in SR doesn't really seem connected to the Donner films. In S2 there is also the apparent killing of the depowered Phantom Zone villains at the end. Don't like that either about the Donner movies. Superman doesn't kill anyone in SR, but his morality and ethics seem to be much different from the comics.
In the comics you have a wholesome, boyscout type, who always make the right decision. In the comics he did kill Phantom Zone villains from another universe, but he agonized over it b/c he believes killing is wrong. That is the big difference in SR. Of all the mistakes he makes, he doesn't seem to actually learn anything from them of even acknowledge that he's made mistakes. He just tries to make excuses. The movie doesn't spend any quality time showing or discussing how he has changed. It introduces a lot of conflict but never actually shows the process of the resolution or lessons learned from the experience. At the end of S2, Superman promises the President that he'll never let him down/ leave again. SR opens with just that, a 5 year absence. In this sense, the SR Superman doesn't seem like he could possibly be the same character.
THe comic version to me is even further from the SR version. In the comics he understands his responsibilities, he understands his position in the world and he has friends and is a happy positive person. Oh, and he also is happily married. Valuing marriage, telling Lois his secret, trusting her to keep it and believing enough in her that she can live with it are very different from both Donner's version and what is implied in SR. In contrast, the SR Superman is beset with problems of his own making, he doesn't seem to understand how his departure will/ has affected his acquaintances and the world at large. I said acquaintances, b/c this version also seems to bemoan the fact that Superman doesn't have any friends. The only one like him is his illegitimate son, and since he has been born, only now does SUperman feel like he has a true place on Earth. In the comics SUperman has many friends as both SUperman and Clark Kent In the Donner films, we see suggestions that he and Jimmy will have a friendship. He and Lois throughout all four original films do develop a friendship even as Clark. In SIII we see Lana and learn that she is an old friend of Clark's. Additionally, he treats them well. He treats them like you would treat a true friend. WHile not spending an inordinate amount of time on the subject it is suggested that he is not the lonely, pity me character we see in SR whose only connection to Earth seems to be Lois and I guess his mom. And we know from SR he hasn't treated Lois well, either before or after he left.
The comics over the years have spent a lot of time fleshing out SUperman's character and friendships. SR takes the approach that he is lonely and doesn't understand his place in the universe and his subsequent actions echo this. The Superman in the comics is the kind of person I would be proud to call friend. The Superman in SR seems like one of those people that just suck the life out of you b/c they can't understand or make any head way in dealing with their own self inflicted problems.