Ultimately, output is about one thing: moving air. The more diaphragm area you have and the more excursion you have the more air you will move and the more output you will get. For this reason, all else being equal, a pair of 10w3s should have more output than 1 12w6.
You have not mentioned enclosures at all and this is probably the most important variable in predicting performance. 2 10w3 will require an enclosure almost twice the size of 1 12w6 so if you dont want to give up alot of trunk space the single w6 will be a better option. If trunk space isnt an issue, id do the the 2 10w3 ported. You could consider getting a single 10w6 and if more ouput is desired you could just buy a second later. Dont get a capacitor. They are an ineffective fix, and a car like yours should have no electrical problem supporting a 1000/1. If money really isnt an issue, id get a 13w7.
As a last note, I would warn you against thinking that just because the w3 is an entry level driver that there will be a major audible difference in "quality" compared with the w6. Price tag is not a determinant of quality. Human hearing is incredibly incapable of detecting distortion in the sub frequency range (20-40hz especially), so if your concern is "quality" what you need to worry about between the w3 and w6 is producing a flat frequency response across the sub's bandwidth. Your prime tool is accomplishing this is enclosure design