1. Shipping a stack of libs that may change over time, but are generally static, inside the jar would have made a 1meg download 4megs. EVERY update. We do lots of those. So an on demand system was created. It lets us update without having to tell you to get x,y,z all the time and deal with that. If that displeases you, I'm sorry. It's how it's going to be. Minecraft is a pretty online game. It's a fairly safe assumption that you're online. If you're not, you can grab the resources and copy them into place yourself. The downloads are easily accessible, both one at a time and as a bundle: http://files.minecraftforge.net/fmllibs/fml_libs.zip
2. What are you talking about? It looks like your mac has made a nice mess of the FML/forge distributable. Use something other than mac zip. It's crap.
3. Mostly they're not a problem and can be ignored. Merging lots of mods into the jar though: that's just a recipe for disaster and we strongly discourage that now. DON'T do it. The mods folder is there for a reason, USE IT. Also, some mods will NOT work inside the Jar at all any more. It may well come to pass that I completely disable this kind of modloading. It's needless and a nuisance. If you want to "manage" things, use a launcher: magic launcher and multimc both work well.