I have driven over 28,000 kilometres in my car and the only real issue is noise from the front suspension, which is going to be fixed under warranty.
Have you considered the manual? I have the 5 speed and I find it easy to row and well matched to the engine, with plenty of overtaking power.
I too had a 2002 civic (manual) and until the 2012 Focus came along every other small car (apart from the expensive Golf) had a driving experience and interior that could not compare. The Focus is comfortable and rattle free and quiet - something I really appreciated after driving the noisy Civic for 250,000 kilometres.
I actually bought a 2012 Civic (auto) for my wife. Very comfortable and roomy, but with horrible fabrics and plastics. One fault too - the interior fan sounds like a bearing is faulty. 40,000 km so far and no other issues.