Yeah, this idea that fantasy can invoke the deus ex machina while SF can't is just, well, garbage. I'm a bit more into SF than fantasy (and, admittedly, into other genres a lot more than either) but that has more to do with an overall level of general quality than anything like this.
I do have to disagree that fantasy and SF share the "what would the world be like if X was different" thing. By and large - and yes, there are many exceptions, the super-awesome Fullmetal Alchemist series being one of them - SF does often adhere to this but fantasy is something totally different. We can pretty well trace the fantasy genre to Tolkien and the King Arthur tales and from there to what the world looked like through the eyes of a medieval person. That world is far, far different than the world we know today. It's not simply "one thing" as in "what if there really was magic"; at its root, it's "what if there really was magic" and "what if all those made-up animals in the medieval bestiaries were real" and "what if the quests of Arthurian legend were real things and not fanciful stories to keep knights in line" and so on. Of course, we've also had several generations of authors expanding on these themes and intermixing them with other genres but that's the root, which is way different from the SF, which I think *is* the "what if X" thing as defined by H.G. Wells' "The Time Machine" and so on.
I love medieval history but my biggest issue with fantasy in general is that there is a *lot* of crap out there. The existence of RPGs and publishing houses by those RPGs are nice in the sense that they get inexperienced authors to start their careers, but the downside is that the vast majority of the books these places produce - pretty well all of them I'd say - are high in milieu but very, very low in character and quite simple in plotting as well. That just doesn't interest me. If I want to read about a cool location I'll buy a sourcebook or read the Silmarillion. SF doesn't have the same kind of support and although there is an awful lot of "Star Wars" type series out there, there are also a lot of just plain good authors in the genre. I mean, fantasy has Terry Brooks and G.R.R. Martin and Robert Jordan I guess, but on an aesthetic level I just prefer Asimov and Philip K. Dick and William Gibson.