Seeing as rumours point towards a largely unchanged chassis for the upcoming AS MacBook Pro, what can you foresee being potential early adopter issues? Software compatibility is the most obvious one, I suppose.
As someone who ordered the first Intel 20" iMac back in February 2006 and remembers what being an early adopter on that transition was like, you're going to have a bunch of software that isn't native. That being said, I don't foresee this being anywhere near as much of a clusterf**k this time around as it was then, especially with Microsoft, Adobe, and Apple's own apps all being pretty much ready to go already. There is also a bevy of Mac software that was needed then that there really isn't a modern equivalent out there (let alone need for) today.
Otherwise, as was stated before, the Core Duo/Solo Macs kind of got shafted in that they were quickly outclassed by the Core 2 Duo Macs. If you bought a Core Duo Mac, you got kicked to the curb one OS release before your Mac's immediate successor. That kind of sucked. So, basically, Rev A you were capped at 10.6 Snow Leopard; Rev B you were capped at 10.7 Lion; and Rev C (and many Revs after) you were capped at 10.11 El Capitan because the requirements didn't change between 10.8 Mountain Lion and 10.11 El Capitan.
On the MacBook Pro side of things, Apple really didn't figure out thermals very well. At least not until the Unibody design some three years into the Intel Era. The first two Revs of MacBook Pro ran way hot for their enclosure (albeit the ATI Radeon Mobility X1600 was more to blame than the Core Duo and Core 2 Duo). The pre-unibody white MacBooks had some issues here too; albeit not as severe nor as often. All that to say that Apple may have additional learning curves ahead when it comes to redesigning their notebooks for the new architecture. However, assuming they are coservative with their early designs, stick to their current designs (at least initially) and largely don't do any drastic chassis thinning, they should be much better off this time around.
As long as someone in the engineering team does a good and proper retrospective of the Intel Mac era from 2006 to present, and goes over every learned lesson with a fine tooth comb, they ought to be much better off this time around.