I felt bad for Conner in how Superman reacted to him, but I still found Superman sympathetic in that situation. Superman had been violated, having basically a child of his created without his consent. I would've loved to have seen that resolved a little more on screen.
YJ brings such a great well developed world, it makes me wish there were room for a spin off series, such as the Justice League. Maybe as a prequel, go back to Year One.