Edit: I originally wrote some defense of responsibly raised food with respect to point 3, which you actually seem to have addressed in the original post.
I believe the other issues are much more complicated than you make them seem, which is to be expected but makes convincing someone more difficult (and makes it way harder to compete against justifications of the status quo). A lot of the meat I eat I can justify from the perspective of animal cruelty (I am fine, for example,being cruel to most of the life on earth, and I am completely fine killing almost all of it), so to convince me to stop you would actually need to win the other arguments. That said, many of the things I eat are in fact inconsistent with my beliefs and I should stop. I've made a tiny effort to change my behavior, but its been basically ineffective. Now that I'm thinking about the issue rationally, I would probably have a lot more luck if I tried to somehow coerce my future self into cooperating. I think I could get friends/acquaintances to help with that...
As I said, the issues are a lot more complicated. I'm supplying the basic gists of the arguments with the intention that people who aren't familiar with them should go find some professional literature to get themselves familiar with them. I'm not educated enough to defend it that well myself (at least, not tonight). Someone who is better equipped can probably beat me in an argument about how precisely it impacts the environment. But beating me is irrelevant - winning arguments doesn't make you right. If you HAVEN'T looked at the environmental issues, ther...
(Note: I wasn't quite sure whether this warranted a high level post or just a discussion. I haven't made a high level post yet, and wasn't entirely sure what the requirements are. For now I made it a discussion, but I'd like some feedback on that)
I've been somewhat surprised by the lack of many threads on Less Wrong dealing with vegetarianism, either for or against. Is there some near-universally accepted-but-unspoken philosophy here, or is it just not something people think of much? I was particularly taken aback by the Newtonmas invitation not even mentioning a vegetarian option. If a bunch of hyper-rationalists aren't even thinking about it, then either something is pretty wrong with my thinking or theirs.
I'm not going to go through all the arguments in detail here, but I'll list the basic ideas. If you've read "Diet for a Small Planet" or are otherwise aware of the specifics, and have counterarguments, feel free to object. If you haven't, I consider reading it (or something similar) a prerequisite for making a decision about whether you eat meat, just as reading the sequences is important to have meaningful discussion on this site.
The issues:
1. "It's cruel to animals." Factory farming is cruel on a massive scale, beyond what we find in nature. Even if animal suffering has only 1% the weight of a humans, there's enough multiplying going on that you can't just ignore it. I haven't precisely clarified my ethics in a way that avoids the Repugnant Conclusion (I've been vaguely describing myself as a "Preference Utilitarian" but I confess that I haven't fully explored the ramifications of it), but it seems to me that if you're not okay with breeding a subservient, less intelligent species of humans for slave labor and consumption, you shouldn't be okay with how we treat animals. I don't think intelligence gives humans any additional intrinsic value, and I don't think most humans use their intelligence to contribute to the universe on a scale meaningful enough to make a binary distinction between the instrumental value of the average human vs the average cow.
2. "It's bad for humans." The scale on which we eat meat is demonstrably unhealthy, wasteful and recent (arising in Western culture in the last hundred years). The way Westerners eat in general is unhealthy and meat is just a part of that, but it's a significant factor.
3. "It's bad for the environment (which is bad for both human and non-human animals)." Massive amounts of cows require massive amounts of grain, which require unsustainable agriculture which damages the soil. The cows themselves are a major pollution. (Edit: removed an attention grabbing fact that may or may not have been strictly true but I'm not currently prepared to defend)
Now, there are some legitimate counterarguments against strict vegetarianism. It's not necessary to be a pure vegetarian for health or environmental reasons. I do not object to free range farms that provide their animals with a decent life and painless death. I am fine with hunting. (In fact, until a super-AI somehow rewrites the rules of the ecosystem, hunting certain animals is necessary since humans have eliminated the natural predators). On top of all that, animal cruelty is only one of a million problems facing the world, factoring farming is only one of its causes, and dealing with it takes effort. You could be spending that effort dealing with one of the other 999,999 kinds of injustice that the world faces. And if that is your choice, after having given serious consideration to the issue, I understand.
I actually eat meat approximately once a month, for each of the above reasons. Western Society makes it difficult to live perfectly, and once-a-month turns out to be approximately how often I fail to live up to my ideals. My end goal for food consumption is to derive my meat, eggs and dairy products from ethical sources, after which I'll consider it "good enough" (i.e. diminishing returns of effort vs improving-the-world) and move on to another area of self improvement.