I think the variation in who gets invited is partly due to regional influences. A program only has so much money to spend and they want to use it wisely and interview people who have a higher likelihood of actually coming to their program(ie ranking them highly). People tend to train in a similar region to where they are from(certainly not always true). So, if I am on the east coast, a higher percentage of people that I would invite would be from my own region. In order to get some diversity and see some of the top quality people from around the country, I would also invite some of them. But if I am smart, I would not invite a majority of out of staters just because the likelihood of matching with them is probably less due to geographic reasons. The more competitive the program and the higher the profile of the program, the less of a concern this would be. Many programs put a lot of effort into recruiting their own students because they have a higher likelihood of staying put where they are. If you spend all of your recruiting money chasing low yield people from across the country, you could end up with a scramble for your program in March.
So basically, if I were doing the inviting and were on the east coast. With 2 equally qualified candidates, one from my own area and one from the west coast, and only one interview spot left to give. I would invite the one from my own region of the country. It is just a higher yield invite.
It is probably wise for most programs to interview at least half of their candidates from their own geographical area. Just shooting from the hip. I am not sure if others share my feelings.
This is my long winded explanation for why it seems strange that you might get an invite from one high powered program but be snubbed by a lesser known program. Another reason is that most programs interview roughly 10 people per position. If the program only has 6 spots, they may only send out 60 invites. If the program has 12 spots, there may be 120 interviewees and so on. So, your chances of getting an interview may be better at the bigger programs.
I hope this helps. If you have a particular geographic reason for wanting to be at a particular program, it never hurts to call and let them know(especially if that is not apparent on your application). It could be the factor that tips them towards inviting you for an interview.