My current solution is this...

Using the old WRT54GL as my NAT Router serving DHCP to the Time Capsule which is running in Bridge mode. LAN devices are all connected through the Time Capsule, wired and wireless. The radio on the WRT is turned off.

First benefit: QoS management - though I didn't notice any problems running congestive downloads and VOIP at the same time with TIme Capsule.

Secondary (but important benefit): I can use Tomato's very nice bandwidth logging which gets saved hourly to my TV server via CIFS.

As long as I'm using the WRT54GL in front of the Time Capsule, I can't think of any negatives to not using the TC's NAT. Or rather, I can think of no benefit to using double NAT.

If I ever find a stable piece of software that can monitor my bandwidth usage using SNMP then I may just give up the WRT. Unfortunately I haven't been able to find a solution that works or doesn't involve installing Apache and all manner of other server software.