I watched the movie twice today, and I really liked it. Is it an epic masterpiece of storytelling? No. Does it have flaws? Yes. Overall, I'd rate it an 8.5/10. Better than Age of Ultron, Thor, both of the Iron Man sequels, the 1st Captain America film, the Dark Knight Rises, both of the Keaton Batman films, TASM2, X-Men 3, Spiderman 3, both of the Jessica Alba Fantastic 4 films (it's virtually guaranteed to be better than the newer one, I just never saw the newer one, so it's not on my list here), Indy 4, both of the new Trek films (and I actually like them both), both Hulk films, and Harry Potter and the Order of the Phoenix. I'd put it on par with the first Avengers film, but below Winter Soldier and The Dark Knight.
Affleck's Batman and Bruce Wayne are amazing. I love how creepy Batman is when we first see him. I think the voice modulator works so much better than Bale's growling while also having more realism than Keaton's doing nothing to disguise his voice. I love Batman's stunt driving. When Bruce was driving to Wayne tower in Metropolis it felt like watching James Bond in his spy car. I also love the more brutal Batman. I've seen some people online complaining about him killing people, but screw that noise. The other good live-action portrayals of batman (Bale and Keaton) both saw him killing at least one person.
I also thought Wonder Woman shined when she was on screen. She is fierce, sexy, mysterious, and everything that I would expect from her given how little she actually appears in the film.
I also liked the flash vision scene. DC has a very rich multiverse of elseworld stories, and I thought the nod to the Injustice storyline (which seems to be the case given that Superman is talking about Lois being taken from him) was great. I also thought the cameos for the rest of the league were good, though I would have put them in the same scene where Bruce sends Wonder Woman the Brussels picture.
On the topic of the cameos, I thought it was interesting that a mother box had already appeared on Earth, as appears to be evident from the Cyborg cameo. It reminds me greatly of his origin in the animated film Justice league: War.
I thought Cavill did a great job as a Superman who was trying to find his place in a world that both loves and loathes him, and fears and respects him. I thought he really showed his morality and humanity in taking Doomsday into space, and potentially being willing to die to save the planet (after all, there's no reason to expect that he would think he could survive being nuked like that).
I also liked Eisenberg's Luthor. He was not the traditional comic book Luthor, but none of the live-action film portrayals have been: the sleazy real-estate obsessed Luthor played by Hackman, and later by Spacey in Superman Returns, is pretty far from the evil 80's businessman Luthor that I loved from the animated series, and could (I believe) hardly be said to be true to the comics portrayals (which have, admittedly, bounced around in their theme as well). The only thing I didn't like about his Luthor on my first viewing was the last scene he was in. However, a second viewing led me to the conclusion that he was sort of like Darkseid's Renfield. A conclusion which seems supported by the "communion" deleted scene that was released.
I think the non-linear nature of some of the story may have thrown some people off, but I didn't have any issues with following it.
I think my biggest issue with the film is the lack of a fully fleshed out motivation for Lex (but that may be in the R rated director's cut). However, I also think the movie didn't suffer much from it given that Bruce/Batman was basically the villain, and his reasons for going after Superman were quite well established.