Silvertop, I think you will find the components easier to install. Yes, there are more pieces, but by having more pieces you gain flexibility in placement. With suitable locations being at a premium, I think having placement flexibility will trump having fewer pieces when in comes to ease. Also, as you said, a good 6x9 is harder to come by. There are a lot more options when it comes to good component speakers.
As far as bass goes, I know *I* can hear a difference between 6.5" round woofers and 6x9's, but I think the average person would be hard pressed to really notice much difference. Also, the enclosure plays a large roll in the bass delivery of any smaller woofer such as we are talking about here. My gut tells me the door will be a poor enclosure, and not big enough anyway to really allow even a good 6x9 to deliver more bass than a good 6.5" woofer (...as part of a component set). Saying it another way, if you want more bass than a 6.5" installed in the door delivers, I don't think you will find a 6x9 installed in the door will deliver enough more to satisfy you - you will need to look at other options.
Speaking of other options, there are quite a few. I don't have my kit yet, so I can't qualify specific areas or solutions yet, but some preliminary thoughts I've had are:
- Sealed box under the dash housing a 6.5" or 8" sub. You wouldn't get a ton of bass with this, but you would need almost no space.
- Ported box housing a 6.5" or 8" sub in either forward of the front firewall, or rearward of the rear firewall, ported INTO the cabin. Would take up more space, but in areas where such space seems to exist.
- Under-seat transducer. Technically NOT a subwoofer, but it would feel like one. They make them pretty small, and they take less power than a sub.