Honda Civic is the most reliable car personally. Yaris been around only for couple of years, while Civic been around since the 70's. Also, you wouldn't need to ever take Honda for any service warranty. Its engine can last up to 105K without major tuneup done (spark plug replacement) so long you keep up with its regular schedule maintenance. I own a Honda now and Hyundai many years back....Honda is your car...not to sound bias or anything
Oh almost forget to mention....Honda keeps its depreciation value better than Hyundai.