agreed, 6x9s are not the same as 6x8s, since the factory speaker is placed into an adapter that sticks out a good bit from the door, there is not really much room at all for the hole to be enlarged. you will want to either stick with the factory size (not really a lot of options for top end speakers) or as mentioned above, for the best sound quality, go with a good 6.5 coaxial or component speaker and an adapter (some even come with the adapter)
if you really wanted to, i guess you could glass your own adapter, but then you would be putting a lot of work into making the wrong sized speaker fit, especially since there are a lot of better sounding speakers that will fit