Likelihood of extra planets in systems identified by Kepler? Kepler has found some systems with multiple planets and shown that it's likely that 7% of sun-like stars have Earth-like planets (video).  I don't think we know enough about extra solar planets to know how planetary systems are organized on average, but the multiple-planet systems are few and would be ones where the orbits of the planets are close to the star and/or flat.  In our own solar system for instance in the small strip of the sky where an observer could see the Earth transit, there are only two small sections where they could also see Venus transit, and if they did happen to see both the Earth and Venus, they would not be able to see any of our other planets transit (up to Saturn at least).  

I wrote a small program to show roughly the visible area of sky where each planet could be seen to transit.  Shown is 4 degrees above or below the ecliptic:



Is there just not enough known about the variability of inclinations in orbits of planets in general to speculate about what percent of confirmed candidate planets might have siblings with different inclinations that we cannot see?  If other planetary systems had varying inclinations in their orbits like ours, it looks like for every 'Earth' they found, any other planets would only have about a 7% chance of also being visible.  Is there any reason to think that other systems with multiple planets might have less or more variability in the inclinations of the orbits of their planets?
There are many planets that Kepler couldn't detect because the ecliptic is inclined so no transit occurs from the perspective of Earth. We are much more likely to see a transit if the transiting planet is close to the star, and so in Kepler's sample of stars, a disproportionate number of the planets discovered orbit very close to the star. It is probable that most stars have planets, and many of those planets orbit much further out than the average in the Kepler sample. And, moreover, the stars which have been found to have planets are likely to have others, orbiting further from the sun, and inclined, so they are not detectable by transits. Kepler has not detected Earth size planets orbiting in the habitable zone of sun-like stars.

So far we do not have the technology to detect a planetary system that mirrors the Solar System. Our alien friends, if they are very close to the ecliptic may detect transits of Earth but would likely miss the other planets. And there is no reason to suspect that the Solar system is not typical in the range of inclination of its planets.