Major - Rear suspension control arm bushings (clunk from rear over bumps).
Minor - timing cover oil leak (warranty covered) - leak on the back of the engine facing firewall.
Minor - intake manifold cold tick (warranty covered) - still ticking after replacement, so I am living with it.
Major - Clunk on the left side over small bumps - turned out to be transmission mount centre bolt loose - appears to be the same issue that plagued the Mazdaspeed 3 (turbo 2.3) - tightened myself to 80 ft-lbs (look at the articles describing how to do the Mazdaspeed/turbo 2007 cars, and then the service manual for the correct torque).
Minor - Belt noise (hissing especially when cold) - just replace the belts to fix - 'gurgling' noise at 1500 RPM warm - replaced drive belt tensioner (there is a 1500 RPM noise when cold - haven't found what is causing that yet - I think it is the EGR).
Minor - rear brakes dragging due to corrosion in the rear caliper guides (pushing rubber guide boots against slide pins, binding rear brakes) - just ream corrosion out.
Major - driver side front strut had a 1 inch "dead zone", where there was no damping - seemed to ride OK - noticed it after upgrading the front struts.
Minor - Aluminum shavings in drain oil - turned out to be from galling threads on the drain plug - a Fumoto valve fixed that.
Minor - metallic click noise when shifting from park to Drive, or Drive to reverse - apply grease between driveshaft and hub bearing mating surface - as per TSB (dealer told me about this)
Minor - 17 inch alloy rims seem to dent easily (inner face - from potholes) - have had to get all 4 corrected at a rim repair place to correct vibration.
Minor - front brake replacement - changed back to OEM when the fronts were pulsing from aftermarket discs/brakes. Note that the front discs will rust onto the outer ridge of the wheel hub - search online for tricks to remove (removed mine in 30 minutes by using the rotor removal trick used by Ford F150 people - putting bolts in the caliper mounting holes to apply force to the rotor and pop the rotor off).