Jaymerchi,
I would have to emphasize that from my experience, IPS's shares far more applicants with the East Coast IR establishment (SAIS, SIPA, and Fletcher) than with the MPP programs, so my relative comparisons will remain with the IR programs I've been accepted to and understand well.
In respects to the "seriousness" of the program, I can assure you that its a red herring issue. Most of the core IPS courses are exclusively reserved for IPS and internal Stanford MPP masters students. Given the small size of the program, there is no chance of overbooked or overcrowded classrooms for the core curriculum. In comparison, students at more established IR schools like SIPA and SAIS often have to deal with quotas and huge impersonal core class sizes, even if the resources are not pooled from other programs. Each IPS student is also given a fully tenured Stanford professor to serve as their dedicated advisors. Very few masters programs can command that level of attention.
The interdisciplinary nature of the program also ensures that you do have the option to take courses at Stanford's world renowned Law, Business, and Engineering schools. Stanford is one of the few universities that can claim the majority of their graduate programs are ranked in the top 10, so the pooling collective university resources available at IPS will only serve to expand your intellectual horizons.
I had many of the same concerns initially, but most of them are due to the relatively weak salesmanship on the part of IPS. Once you dig more into the program, you will know why so many chose this younger program over many more "reputable" IR schools. Finally, initial rejection followed by greater WE cannot hurt your chances so do not worry.
