Yeah. I just recently described the path from 2011 to now to someone on reddit, and it took me five paragraphs to explain the co-existence of the pre and post Flashpoint Supermen, how they combined, and why Lex is Superman. I didn't even get into how poorly I think they combined...
Like I said in that comment: "there's good comics involved at every single stage of this operation, but when you look at the whole thing as a single arc, it kind of looks like DC has no idea what they're doing."
I love this show. It's a shame that it only got two seasons; it was just as good as The Batman or Teen Titans, which each got five, but so few people seem to have fond memories of Legion of Super-Heroes. Still, nothing can take away my own affection for this awesome show!