I've had a 2.2 diesel Civic for 18 months now and I am counting the day until I get rid in another 18 months.
Fuel consumption is the main issue – no matter how I drive, it barely gets above 40 mpg. People have told me it will get better with age. I have now done about 40k and have seen no improvement – if I drive like an OAP I can sometimes get up as high as 45 mpg. The Octavia I had prior to this driven in a similar manner would give about 70 mpg.
And the Skoda is probably the biggest issue I have with the Civic – in comparison to the Octavia everything about the Civic is slightly wrong – the turning circle is akin to that of a bus, the 4th 5th and 6th gears are too close in ratio, the sat-nav was 2 years out of date when I got it and they want £195 to update it, the computer gives less useful information, the cheapo plastic petrol filler cover, folding mirrors which don't fold when you lock the car only when you press the button inside. I could go on. Most of the issues are minor niggles but when you have to live with it everyday they build up to a major annoyance.
The only reason I didn't get another Octavia was because of the less than helpful main dealers close to me. I probably won't let this stop me next time.
Get the Jetta if it suits but definitely look at the Skoda and avoid the Civic.