The specific details of the image of the Flying Spaghetti Monster might have been irrelevant to the original satiric purpose. But whether by chance, by Bobby's design, or by divine revelation, the Flying Spaghetti Monster's depicted physical form has a lot going for it as a reference point for post-modern contemplation of divine supernatural intelligences and their role in our universe and/or in our thinking.
Auntie Dee Dee already called out some of the high points -- most important, the noodliness and the multiplicity of appendages, implying unlimited powers of undetectable intervention along with a certain arbitrariness of form; but also the protein orbs whose function we can only guess about (we all have opinions, but it's impossible to resolve them definitively, as is true of so much of religion in general); the flying (remoteness, ambiguous size, and mobility, but wingless -- what use are angels' wings in a universe that's mostly vacuum?); and the paradoxical "always invisible, but looks like this..." nature overall.
Even more important is what the FSM isn't. First, it isn't a static figure. Invisible Pink Unicornism is intended to discount the idea of any god's existence, and the IPU as an image helps to convey that: a unicorn, in our current culture, is a rather trivial and ineffectual beast. It might poke someone with its horn but it probably won't, it'll probably just sit there, comforting in its familiarity but inert, like a figurine on a little girl's nightstand. The FSM, by contrast, by virtue of its noodly appendages, is a dynamic creature, potentially capable of touching anyone or everyone at any time, or always, as your beliefs incline. Second, it's not an animal or a tree or the sun or a galaxy or any other nature symbol -- we leave those symbols, respectfully, to nature worshippers, as the FSM is a creator god and that implies distinguishing the creator from the creation. Third, it's not a human being, which helps steer clear of many temptations to presumption and hubris. For instance, if the physical image of the creator were that of a human king, would it not be tempting to assume that the creator will resemble a human king in other respects as well -- such as being influenceable by flattery, being prone to becoming violently insecure if ritual safeguards aren't observed, and being pleased when you smite the subjects of some enemy king across the border? Or if the creator were to resemble your mother... well, you get the idea. Fourth, it's not an abstract concept, like love or entropy. While one's idea of the FSM (or any creator god) might encompass such abstract concepts, it appears that many of our puny human brains prefer a more concrete symbol (if that's not an oxymoron), something you can draw a picture of, to focus on.
With those four "what the FSM isn't" constraints, it's pretty much a monster by process of elimination. That is to say, the FSM is a physically embodied active being that's not a person or animal. Lovecraft invoked monstrous forms when he wanted to convey the "true horror" of existence, divine horror beyond depiction by ugly-dude part-human representations like vampires or ghouls. (And the FSM has been compared, physically, to Cthulhu; do a search on Cthulhu to find the threads.) Why not use an equally monstrous, but cuter and more benign, form to convey the "true joy" of existence beyond depiction by part-human representations like angels or avatars?
For some additional viewpoints on the "is this all a joke" question, I like to refer people to this thread. It starts out slow, but it's worth reading all the way through.