That's a very fair point, and I think that's where Snyder fell down - what we know now with the benefit of hindsight is that he had a full story arc in mind which spanned BvS and JL and so on. He wanted Superman to struggle with acceptance by humanity (MOS), then to sacrifice his life for them (BvS) and in doing so be embraced by humanity, and then to return with new found optimism and hope (JL). It's a typical resurrection type approach which we've seen done before with many characters in many films.
Of course, watching MOS in 2013 (or even watching it now in isolation).......... none of this was apparent and whilst I generally like Snyder as a director, he did get ahead of himself a bit.
There's nothing wrong with planning story arcs over multiple films and many have done it before successfully. But when it means the key character traits associated with your main character are hampered by limiting their scope to the extent of each film, it introduces problems - especially if you don't get lucky enough to get sequels greenlit or for them to proceed as you originally planned.
There's certainly an element of that. Batman Begins was a real turnaround point for WB and I think they felt that same gritty, back-to-basics and semi-realistic approach would work for Superman too. And with Nolan as a producer on MOS, there was always a chance it would have a Nolan feel at points.