It seems to work now. Boot loader needs some more work, but MySensors part should be usable. If someone likes to have a look you can find it at http://github.com/kisse66/MySensors fork. By default it still uses SPI flash and works just like the original. To use I2C EEPROM uncomment (MyConfig.h) or define MY_OTA_USE_I2C_EEPROM in your sketch. You'll need also MY_OTA_FIRMWARE_FEATURE of course.
My code uses Wire library for I2C (new driver) and defaults to address 0x50 (real I2C address 0xA0) that most EEPROMs use I think. EEPROM has to use 16-bit addresses, 24(L)C256 or 512 should work.
Only tested with MYScontroller, pro mini 8MHz with nRF24 and 24LC512 EEPROM on AVR HW I2C.
Do note that I'm still working on the bootloader part which you'll need to make this actually work. I have a "seems like working" hack, but it needs some more work. Approach is to use DualOptiboot code and add option there for alternate I2C. I'll publish it when it's getting a bit better.