You keep forgetting the most important thing: people could take their 32-bit apps with them and run them on their 64-bit machines. Immediately. No modification, no reconfiguration - the hard yards were done by software vendors. People cannot do that with their IPv4 addresses and connections and IPv6. Everything has to be done (essentially) from scratch. Software upgrades alone do not help.
Some people mention things like toredo and other 4/6 cruft. What good does that do, when you get _different_ addresses, so if you have things like DNS, firewalls, services etc. set up, you have to do it all over again. It is completely different. In fact, the simple fact of needing to _think_ whether and what you'll need to do is sufficient to show that this has been handled poorly.
Of course people start switching only when the need to. That's why many folks still run 32-bit OSes and apps on their 64-bit machines, without even knowing or caring they are really 64-bit. And yet, pretty much any server, PC or notebook you buy today can do 64-bits. If IPv6 transition was handled the same way, most folks out there would not even be aware there was a transition. They would already be on IPv6, not caring one iota about the new connections having real IPv6 addresses. They could still see everything, just like they always did. And these new connections could see them just fine.
Just go talk to your average network/system admin out there. Most of them have absolutely no idea what to do. If they introduce IPv6 to their network, they will have to spend years battling two completely separate setups (essentially, they are building their network from scratch). Initially, for no benefit at all. This never happened with amd64.
If you told them that to get IPv6 support, they needed to install at least version x.y.z on all of their equipment or even just change the equipment and reload the config, that would be way easier.
The amd64 example shows nicely how the market does it with minimal disruption. Remember, even Intel, the leader in the field, had to succumb to an architecture designed by an inferior competitor.