There is a reason why round speakers are preferred in the aftermarket. Round speakers are technically better sounding. 6x9's produce more bass because of large surface area (as compared to 6.5" round speakers). However, for good midrange/midbass (esp. vocal separation), 6.5" round speaker inherently is more stable and produce clearer sounds. This is why top-end speaker combo (midrange and tweeter) comes in 5.25" or 6.5" round speaker. This is also why you don't see 7" or 8" midrange speakers...again, too big for it's own purpose.
For aftermarket systems, you would want a tight midrange with good vocal separation from your door speakers. Bass is handled separately by an independent subwoofer.
For the 4runner, Toyota does the short-cut version. That is, they install 6x9 speakers in the front door to handle midrange duties AND produce bass at the same time. For JBL-equipped 4runners, the small subwoofer in the cargo area is not meant to produce earth-shattering bass to the front driver...it's more for the rear seat passengers and to provide bass "ambience" thru-out cabin. Because of this limitation, the 6x9 speakers in the front doors are made to produce it's share of bass...provide punch up front. I am sure that the 6x9's have their frequency cut lower (thus, more bass) than the average aftermarket midrange. However, by doing so, you are sacrificing a little bit of true midrange clarity and separation that can only be produced by a classic round speaker.
BTW, the same principle applies to the optimal size for tweeters. For the best high-frequency sound, 1" tweeters are the best. They are big enough to overlap to produce enough midrange frequencies with the midrange speaker to produce uniform sound. 0.75" is about as small as you would want. Anything bigger than 1" will result in decreased definition of high-frequency voice. Anything smaller than 0.75" will be too limited to match with a midrange speaker.
Hope this helps.
