I like Karmagen a lot, but build points are the most common way to make a character. After all, build points are in the main rulebook, while Karmagen is one of two optional methods presented in Runner's Companion.
A few things conspired to make Karmagen less popular. The original version created characters who were much more powerful than characters created with build points (the claim by someone who worked on it is that the 750 Karma was originally intended to be used with the x5 Attribute multiplier), and the "free" metatype costs irked a lot of people (even though metatypes such as orks equate to a net gain under build points, too). Then SR4A came out, putting Karmagen in limbo. Heck, there still isn't an official errata out for Runner's Companion, although I hear the newest copies have it (Attribute costs are x5, and you pay your metatype cost in Karma - 30 Karma to be an elf, etc.).