In the end it seems the struggle was not between men and animals but between the just and the unjust, between those driven by ideals and those driven by greed. The greedy and unjust certainly win as all the figures of integrity are defeated, one by one. Snowball and Boxer leave the farm in ways that are rather extremely negative and with their departure we see the triumph of the commercial and amoral values which were attributed to Farmer Jones.
In the final scene, it seems as if the humans do, since they have "converted" the pigs over to their way of thinking and being so much that they cannot even be distinguished from one other anymore! For the animals looking on, this is a devastating revelation. They are no better off at this point than they were with Farmer Jones before the revolution.
What is the cruel "lesson" to be learned from this? Perhaps that the options in life are simple - either be 'bought off' by the system by conforming to it and compromising any inconveniet ethics along the way or be exploited and "punished" for following one's idealism to its natural end.
The old adage "Might Is Right" holds true in the Bolshevik-Menshevik aftermath of the Russian revolution, and it is only too pertinent in light of globalisation today. There is no place for the little guy...
I would hazard a guess that the major theme of the story is not related to who wins, but to who loses --- the animals. This is true whether the original tyrants come from without our genre (humans), or from within the animal genre (pigs) --- the lowest class, the animals, get the short end of the stick either way. The humans promise nothing, and that's what they deliver; the pigs promise all kinds of benefits, but it turns out that they benefits are for them, not for the animals. I read the book not so much as a struggle between animals and humans, but between the haves (whoever they happen to be at any given moment) and the have nots. It is important for the have nots (animals) to avoid trusting anyone who promises them any benefits because those in power are often more interested in the power than those who gave it to them.
The animals win the three battles at the farm--first they run off the humans almost by accident. Then there are two official battles which the animals rise up and succeed in winning together.
Ultimately, however, the humans win. This is because the pigs who are in charge of Animal Farm (which was originally and then later becomes "Manor Farm" again) become indistinguishable from humans at the end of the book. They have done all the things that Old Major said they should never do--they moved into the house, the sleep in the beds, they use sheets, they drink alcohol, they kill other animals for speaking out against them. The pigs become the "new" humans at the farm, and the other animals are working harder for less compensation under the pigs' rule.
The pig/humans win the struggle because they keep the other animals in the dark and also under their control with propaganda techniques--songs, Squealer, and the alteration of the rules painted on the side of the barn. Eventually, the rules simply read: "All animals are equals. Some animals are more equal than others."
The pigs are the ones who are in control from the beginning because of their intelligence. As the book progresses and the pigs assume more freedoms and luxuries, they continue to want more until such time that they are the new humans running the farm.