As Solarius suggested, the "549,755,813,888 ways to play Openxcom" was a jab at the sort of silly, excessive statistics that get thrown around in commercials and ads. For Enemy Unknown, Firaxis could easily have tallied up their 4 difficulty levels, ironman mode, and 12 Second Wave options and legitimately claimed that there are 131,072 ways to play Enemy Unknown. It is true, but it's meaningless - who's going to play a game that many times? I don't find a stat like that intimidating though, it's just ridiculous.
While the options vs. mods issue may merit further discussion, it's more of a matter-of -onvenience issue at this point than a playability issue. Could the options stand to be cleaned up and reorganized some - probably, but everyone would have their own ideas about how it should be done (as this topic is starting to demonstrate.)
Hobbes, I don't think your fear of overloading the player is baseless, but I'd imagine most new players are probably going to either go with just the vanilla settings until they learn the game or ask around the forum for recommendations. While the many options and modibility are selling points of Openxcom, the game itself doesn't make any effort to push you toward changing the default options. To me, the advance options and mods are something like Second Wave, they're there to give some more variety and customization for people who have experienced vanilla.
i admit perhaps here in "why is openxcom great"-thread is the wrong place for such
Yeah, this thread is derailing pretty badly.
To tie it back into the topic, I'd say that the fact that we're debating the layout of the options menu as one of the bigger issues of the game is a testimony to the success of Openxcom. Option layout preferences are a pretty big step down from base disjoint bug and 80-item limit.