Sensor default output:
After power up OV5640 sensor will not have any output signals. There are several registers (refer to the datasheet) that are responsible for enabling pad outputs. Thus, the registers must be configured before getting any output signals from the sensor.
Potential I2C Communication problem with ZC702 board:
I had communication problem with OV5640 sensor. After investigation, it appeared that there is a slave address conflict between the image sensor and HDMI controller that is on the ZC702 board (which may also be the same chip on the Zybo). The solution was to disable channel 1 of the I2C mux, and allow only channel 5 that is routed to the FMC connector.
It is worth mentioning the OV7670, that I would expect to have a slave address conflict due to the I2C port expander that is also on the board and is on the channel 3 of the I2C mux. Thus, it must be disabled to allow only addressing the image sensor.