On the bottom
Headphone jack on the bottom makes sense, like the iPod Mini and the iPod Touch.
The headphone jack won't include composite video. Apple originally did that on the video iPod, then quickly removed it on the next iteration. The headphone jack has a tip and 3 rings: ground, right, left, and microphone. No space for composite video there.
Heck composite video inputs are starting to get harder and harder to find. My Sharp Aquos LCD TV requires a special (non-standard, but still easy to get) cable to support composite video.
With Airplay and being able to access the video files over the dock connector, everything is moving digitally.
While I think the correct thing for Apple to do is to use a micro-USB connector (as mandated by the EU), I don't think they will. The fees they get from the manufacturers for a proprietary connector is just too appealing.
Although, if they did use micro-USB, they could potentially use the same trick they did in the gum-stick version of the iPod Shuffle, where they had extra pins in the USB jack (behind and between the standard USB pins) for audio output. This arrangement would still require a special cable (possibly chipped) for the extra audio/video features, but a standard micro-USB cable could be used for charging and syncing.
It'd be neat to have USB3 support as well. I doubt there'd be Thunderbolt syncing. Most PCs (Windows and Macs included), do not have Thunderbolt built-in. My almost 3-year-old MacBook Pro (that I just put an SSD in to extend its life), and my 24" iMac do not have Thunderbolt and I would be disappointed if that were the only way.
Note that the latest iPhones support WiFi Syncing when charging...