First off, are they expecting to make another season? Because if it's not planned for sure, then WHAT was up with that little bonus scene (plus all the unanswered questions).
That aside, I really really enjoyed this season. It scratched a very specific itch I have for superhuman/experimented on heroes, giving me almost exactly what I wanted. However, I do think that the first season had better emotional arcs for the characters and more overall heart throughout.
I think this season could've given us what the first season did if they had a few more episodes. Usually I'm in favor of less episodes because some dramas take way too long to get to the point, but in this case, I would've liked to spend more time with these versions of the characters and to see the different relationships between everyone.
I also think that Lady Maeda should've been introduced sooner. We should've seen more of her with Seungjo so that when he kills her the impact would've been greater. I also think her twisted relationship with Taesang was a missed opportunity. It would've been interesting to see more of them throughout the years and actually see what kind of games she was playing with him. I think this would've given us more of an idea of why she had set up such an elaborate scheme to make Taesang kill Chaeok.
All of that to say, I really liked this season and if another season does happen, I'll be eagerly waiting for it.