The reason why other Arduino Wire libraries doesn't work with the Edison is because they call Wire.cpp and it at the same time calls twi.c. The last one calls avr/io.h and avr/interrupt.h, those libraries are exclusive to Arduino's AVR architecture, so they won't be compatible with the Edison's x86 architecture.
Edison uses an Intel modified version of the Wire library so it can be compatible with its architecture. However this is not the only way Edison can use its I2C capabilities. If you use the Edison's Linux side you can find other options apart from the Arduino library.
I am trying to interface adafruit motor shield v1.1 with intel edison board but the AVR and pic32 files are not compatible with intel. Is there any other way to use my motor shield v1.1 or is it better to use the next version v2.1 which have inbuilt i2c?
It's not impossible to use the motor shield v1.1 with Edison but it does require more work since you will have to program it manually however I'd suggest you to choose the Adafruit* Motor Shield v2.0 since it's been officially validated to work with Edison in Intel® Galileo and Intel® Edison Board Shield Testing Report.
Thank you very much for your reply.