I also recommend you do 8's instead.
A 6.5" speaker will generally sound much better than a 6x9, because the sharp corners of the 6x9 stretch the surround in a non-linear way, causing a limitation in cone travel (as mentioned) and distortion. Some morons confuse the distortion as extra bass and thus let their minds believe that it has to be better because its bigger. Its not. trust us.
Put a 6.5 or 8 of good quality in your door and you will be much better off. If you dont have enough depth for mounting a big speaker, look into the kicker RMB8's, these are amazing drivers - tons of midbass and very very thin.