Also talking out of Civic ownership experience. I own a 2009 VXi hatch automatic. Comes with a couple of extras the manual didn't at the time, including USB / Aux input, auto wipers and lights and rear PDC. Also has a different front grille and gloss (instead of matt) spoilers around the lower-body, sometimes colour-coded to the body as well. The auto isn't as sluggish as most people would believe - my bro-in-law drives a manual (bought his 2 months after mine) and I've driven both now. Power delivery is pretty much the same as the manual.
As Creature mentioned, I can't comment on the actual maintenance costs, as I have a full maintenance plan. What I CAN comment on however, is that repairing this car is insanely expensive. I had a small bumper-bashing beginning of June (with very minor damage, only a couple of scratches and slightly bent rear-bumper), but unfortunately had an incident with a security gate that same month (damage to the front bumper, both right doors and rear fender). All in all the repair costs came to just over R61k to replace both bumpers and doors. Obviously, the paint (metallic grey-ish / charcoal) made up almost half of that bill, so consider a non-metallic colour like black, red or white (although the white was only introduced with the auto and facelift in mid-2009).
The car is an absolute joy to drive. The suspension is a bit hard, so driving on uneven surfaces (which is the majority of Midrand) and dirt-roads tends to rattle you a bit and make you feel utterly emphatic for the poor car, but it still hasn't developed rattles or squeaks in the interior. I have had to replace both rear suspension struts due to the bad road conditions though... But that was replaced under warranty. Funnily enough my bro-in-law wen through the exact same thing, with Honda Westrand stating something about a factory fault in the rear suspension. But it seems to be sorted out now.
TL;DR - Very good / comfortable car, auto has extra features, expensive repairs, go for non-metallic colour, hard suspension, possible rear suspension issues