Here's my 2p's worth, as (very briefly) I had the same dilemma.
Essentially you are making the choice between a Honda and a Ford under a different name (remember the Mazda 121? Identical to the Mark IV Fiesta) - no competition. The Civic looks far better, the interior and dash is far nicer, and is far more practical than the 3. The ES and EX are as well specced, if not better. As for the faults, I have an 07 plate and they all seem to have been ironed out; I've had none of the problems you listed on mine.
I went for the diesel Civic; it was more expensive but what clinched it is that the 3 Sport will do about 35mpg, whereas the Civic can get 50mpg plus. With the miles I do, that works out at about £400 per year saving on fuel costs. Plus the Civic costs £115 per year to tax, the 3 a whopping £205!
Ultimately it's your choice, but if you do choose the Civic, go for the diesel.
