Why We are Alone (So Far) in the Galaxy

So, I was just reading this article, because the headline reeled me in. “Gaping Hole in the Solar System?” Well, with my usual over-literal interpretation of things, I thought “Bloody nonsense. How can you have a hole in space? That would be like saying a rose

is not just red, but red with a red spot on it or there’s a river in the ocean.” (which actually exists, so I should just shut up)
Of course, they weren’t speaking about a literal hole. The point of the article is that in a high percentage of the exoplanet systems we’ve discovered, there is a large (like Jupiter) planet very close (like closer than Mercury) to their sun; a high enough percentage that scientists are wondering why we are different. The theory in the article is that once upon a time Jupiter was closer in, but got pulled back out by Saturn. Personally, I suspect it might be because of our detection methods. If we’re looking for that little distortion of a star’s light to indicate presence of a planet, large planets in tight orbit are going to disrupt their sun’s light the most, therefore be the easiest to detect.
The article suggested an answer to another question, however, one that bothers me a lot. If extraterrestrial intelligences exist, why haven’t we been visited yet? Assuming there are 100 billion stars in our galaxy (a conservative estimate), and assuming that one out of a thousand of those solar systems has intelligent life, that means there should be 100 million different species who are potential members of the galactic federation. Puts Star Trek to shame. Surely, a couple of hundred of them should have discovered us by now.
But, if a Jupiter sized planet close to the sun is the standard pattern, then the outer planets of that system might be living in shadow, and therefore be too cold for life, or are being bombarded constantly by asteroids, thus putting a serious limitation on the L factor in the old Drake equation. Maybe we’ve only survived long enough to evolve intelligence because we are between the Sun, giver of heat and light, and our big brother Jupiter, absorbing all the asteroid hits for us.
Maybe we are a freakish case in the universe, product of a system which only occurs once in a billion solar systems – in which case there would only be about a hundred or so intelligent extraterrestrial species, and it’s entirely possible they just haven’t got around to discovering us yet.