I used to babysit a child who didn't play well. She had been pretty much exclusively cared for by her grandmother since birth and hadn't had much of a chance to play with other children besides very limited interaction with strangers in the playground, up to age 5. There was a language barrier too. She would arrive at my door in full character as Scooby Doo or some other tv persona and DD4 could either take it or leave it. (She was able to pick up a bit of whatever was on tv or follow the plot somehow). DD4 (same age and in class with this child) being the youngest in my family was used to being something of a follower but occasionally she looked a bit 
at all the barking and the ghosts and monsters and secret tunnels.
When they went outside to play they would make collections of insects, sticks, stones, worms, slugs, etc., and needed boxes and containers and other items from the house constantly -- I know DD4 wasn't behind any of this. She was a girl who if left to her own devices liked the swing and her scooter and was happy to draw or play with chalk or do puzzles, and the DCs all knew I wasn't available at all times to drop everything and instantly supply bits and bobs they needed for games. I gradually weaned her off the idea that I was her right hand man waiting for the next instruction to facilitate her imagination and introduced the suggestion of making do with what they had to hand, in the shed or elsewhere outdoors, for homes for their various captives and collections. I also introduced her to skating, scootering, riding a tricycle (she hadn't done any of these things at home as her grandmother was afraid she would bolt or fall).
At age 7ish she discovered various fantasy book series such as Eragon, Harry Potter, etc., so thankfully the Scooby Doo days were firmly behind her. Initially she annoyed the other children in school with that just as much as she had with the Scooby Doo thing, but over time she found one or two kindred spirits who also loved dragons. She learned through rebuffs, often quite blunt, in the school playground that not everyone was as enamoured with things that fascinated her as she was, and that even the kindred spirits liked to talk about Other Stuff sometimes. She figured out how to negotiate, to read others a good deal better than she did when she was 5 (at that age she behaved as if she was about 3 with the intellect of a 7 yo), to co-operate better in games of make believe that others started, and to function better in a group. She is still quite a 'strong' character but that will stand to her in the end of course.
For her it was a matter of practice with other children and the grandparents accepting that she would be upset and frustrated several times a week and expecting her to get on with it. They were happy with her progress and had recognised that there was a problem -- she really was very full-on and persistent but allowing her to dominate their days was something they had brought on themselves in many ways; the grandfather was more tuned in to this than the grandmother but they both said it to me. Their hope for her in school was that she would become more rounded socially and learn English.
I suppose my point is that children are a bit hardier than they appear and that parents need to keep the goal of a child who can function in a group in mind and not let various blind spots of their own keep the child back from developing on the social and emotional front. Children can learn a lot from other children and will develop resilience and social skills if they are allowed to.
I would be concerned about a bruise and black eye. I would also be concerned about comments that are nasty and children allowed to exclude others. Whoever is in charge needs to be a bit more watchful than that and try to create a better environment, and leadership is very important as Justabout says. However, I would not expect every child to like a child the way a parent does, and parents should expect that their child will learn that by experience. You don't do a child of 3-5 a favour by allowing them to persist in behaviour that doesn't take into account the ultimate goals of functioning in a group and self care including dressing and feeding.
Since feeding is a problem, I wonder if it would help to bring him to nursery for breakfast instead of afterwards. That way, he might learn to feed himself as the others do and he would not be seen as the latecomer. How disruptive is he to breakfast time, and what does the disruption consist of? How do the staff deal with his disruption?
Would a Montessori nursery or school be an option for your DS? An element of 'self direction' can be better accommodated in the Montessori setting than in a more traditional nursery or school environment.