It isn't though, the story is there and the characters are there and are good, in fact much better than the Marvel and Star Wars movies that have been so acclaimed this past year, all of them.
It's subjective. The story is there...literally, but some find it boring. The characters are there, some don't like how they were used in the story. Is it better than the MCU and SW films this year? I don't know. There's no way to factually determine if something is better, but clearly a lot of people didn't enjoy the film. I didn't, and I consider MOS the best Sups so far.
You need to introduce time travel now? Yeah the general audience had no idea how he was, that left them confused, and that's ok, if the straight forward story of the movie left them confused then I expected no less, but it's not the storyteller's fault.
The flash's identity is irrelevant, it was just a dude warning him from the future.
Building blocks. The same reason the MCU didn't release Iron Man and then GOTG with Thanos and a talking Raccoon. There is only one DC film prior to BVS, about an alien on earth, MOS. That's the world the audience knows going into BVS. Batman is a human who sees an alien as a threat, we can understand that because the humans in MOS had never encounter such a phenomenon and some didn't trust Sups. That's well established and specific to this universe, as opposed to people loving Sups in the Reeve films.
So, in a film that deals with these two elements, all of a sudden, a man shows up from the future (supposedly) in what could be a dream or a vision, with no prior set up. The worst part is, a percentage of the audience doesn't even know who or why this guy is showing up, which creates more questions that the story doesn't bother to answer. The same can be said about the Darkseid references. Why include something that will go over people's heads? If it was properly introduced and established like a good story does, it wouldn't be a meaningless or irrelevant dude, it would be FLASH (OMG!) telling Bruce something important that will have some kind of pay off in the movie.
Your film and story should establish the rules and limitation of that world. People have seen time travel depicted in other movies, but it's kind of lazy writing to throw something in BVS, assuming people are familiar with it because they've seen it elsewhere, thus in a way letting other sources do the job the BVS writer should have done better. Honestly, you could cut the Flash cameo from the film and just leave the nightmare dream, and the story in BVS would still work the same.
Ultimately, it's a filmmaker's job to tell a good story, and Snyder isn't very good at it...it seems. Flash showing up in some time or interdimensional travel to tell Bruce something while he was dreaming (maybe) with no prior introduction to the concept of time travel in that universe it lazy as ****, and confusing for the general audience who had no idea who the bearded guy in a red metal suit was... 
