There are a few things I want to say about this.
I've watched a lot of WLC debates over the years and at this point there are only a few people who would make me excited enough to watch another Craig debate.
Sean Carroll is one of those people.
I'm a huge fan of Dr. Carroll, primarily because he's a cosmologist that is philosophically informed. He organized a Naturalism Workshop with some of the best naturalist scientists and philosophers alive and made it all available online for free (you should watch it). He's an outspoken atheist and naturalist, but more importantly he's a great communicator. I can watch the man give talks and afterwards I always feel like I'm better informed because of it.
If you clicked the link to Dr. Carroll's blog you'll see that most of the things he's read are predicting that he'll get clobbered. Dr. Carroll has stated he isn't aiming to win the debate, but rather to "say things that are true and understandable, and establish a reasonable case for naturalism, especially focusing on issues related to cosmology".
I don't think Carroll is going to get clobbered and I think he should be optimistic. I want to present a few reasons why I think Carroll will do great, some areas of concern, and some humble advice.
Reasons to be Optimistic
A Focused Debate Topic
The debate topic is "The Existence of God in Light of Contemporary Cosmology", which means that it should focus the debate down onto a small subset of arguments in Carroll's area of expertise.
This is a huge advantage to the atheist right off the bat. Apologetics in a debate works best when it's allowed to cover a variety of topics in a debate. This is because the arguments are designed to be simple and intuitive, but they don't hold up well under continued scrutiny. Being able to focus on a specific argument or a limited subset of arguments means that the atheist can hone in directly on the weak points, which prevents the apologist from jumping to other topics that weren't addressed as strongly because of limited time.
In fact two of the debates where Craig clearly lost are the ones where topic was extremely focused. The first is one on "The Problem of Hell" vs. Ray Bradley and the other is "Is God Necessary for Morality" vs. Shelly Kagan.
Dr. Carroll has the Expertise to Win
Simply put, he knows the science and philosophy well enough to hang with Craig on the Cosmological and Fine-Tuning arguments, or at least I think he does. Contrast this with Lawrence Krauss who is an expert in cosmology, but he has an absolute disdain for philosophy. This let Craig run rings around him, at least in their first debate. In the second series of debates Krauss did much better, but I still cringed a bit at some points.
Contrast that with the way Sean Carroll nails it* in his last debate** with Hans Halvorson that you can watch here:
*This is meant to praise Carroll and not an indicator against Halvorson, who came off way better than most apologists I see in debates because he doesn't try to distort science.
**I say "debate" but it was really a discussion given how much the two agreed on things. Hans correctly let go of the cosmological and fine tuning arguments and stated the argument for theism was more about values, meaning, and purpose.
Reasons for Concern
Doing these debates is pretty much Craig's job
In fact it's not just his job, Craig literally has a team of people that research what his opponents have written on topics related to the debate. Read that article and you learn that he puts all other work on hold when a debate is lined up and just prepares. Craig's goal in life is to make Christianity seem intellectually respectable and winning debates is how he goes about it.
Sean has mentioned that he's not going to do insane levels of preparation, and that's fair. What he has to realize is that Craig is going to do insane levels of preparation.
Craig is much more conservative than Halvorson
Sean should be aware of the massive gulf between Craig and Halvorson. Craig pretty much embodies the "Bioloa Style" of apologetics, not only does he argue for the defensibility of theism, but he tries to spin things so that "science really points to god's existence".
Where Halvorson was accommodating of the idea that naturalism has plausible answers to the cosmological and fine tuning arguments, I highly doubt Craig will make any such concessions.
The reason I'm concerned is that while Dr. Carroll says he's going to try and build a positive case (like he did with Halvorson), Craig will make the debate necessarily combative by challenging what should be uncontroversial scientifically speaking. If he's not ready to fight back then Dr. Carroll won't come out looking well.
Craig knows enough cosmology and philosophy to be dangerous
One thing Craig is good at is trying to find some philosophical nuance in order to at once avoid problems for his theology that arise in modern cosmology (see his rejection of 4D-Spacetime for a Neo-Lorentzian view). Further, he will attempt to find some philosophical framework from which he can discredit cosmological theories he doesn't like.
A point of interest here is how Craig is trying to deal with Roger Penrose's Conformal Cyclic Cosmology (CCC) model. Penrose is rather explicit in this being a "past eternal" model, but Craig is working with another apologist (and physicist) Jim Sinclair to try and show that on the CCC model that universes shouldn't be considered temporally ordered, but more of a multiverse scenario. He's not going to do this with anything in the model, but rather by making certain (purely) metaphysical assumptions going in, and then interpreting the model in that light.
This leads into my last section.
Some Humble Advice for Sean Carroll
I'm not an expert in cosmology, so it seems quite odd to try and offer advice to Dr. Carroll. However as someone who has followed a lot of Craig and apologetics in painful detail, I think I can give a few pieces of humble advice that I think could help:
Don't let up on the coherence of Naturalism
Your presentation with Halvorson was awesome! Hammer home the point that not only are there multiple plausible naturalistic models of how the universe exists, but that there are different models for different ways the universe could exist in a naturalistic framework.
Getting Craig to admit to that on stage would be a huge point in your favor. A large part of his appeal is that he lets conservative evangelicals think that science shows "god must have intervened". Disabusing people of that notion alone seems trivial, but in the evangelical world that's a huge step.
It may be best to pick a few models that are defensible and prepare for criticism on them, this is probably an easy one for you.
It will all come down to Time
I'm not talking about debate tactics, I'm talking about the idea of time itself. The standard way Craig looks to discredit many cosmological models is to simply assume that A-Theory of time is correct, and try to argue philosophically that this makes the model untenable.
Please be ready for this and identify it early on in rebuttals. A lot of the time this is the basis for Craig's objections and it goes over most of his opponents heads.
Specifically, look into Craig's "Neo-Lorentzian" interpretation of Special Relativity to try and save the A-Theory of time, and be ready to defend a B-Theory or space-time realism point of view that seems to be implicit in so many cosmological models.
At a minimum, please point out that Craig's endorsement of A-Theory is based on largely theological positions, and backed up with purely metaphysical assumptions. (Reference from Craig's writing).
This is another area where I think you're at advantage, given your work on the topic of time.
Sweep the Leg!
I know you said that your goal is to present a reasonable case for naturalism, but please consider going on the attack at least a few times. You've given talks about how important empirical investigation is and the failures of a priori metaphysical reasoning. Craig is especially vulnerable here when it comes to his endorsement of the Neo-Lorentzian view. He needs the existence of an undetectable privileged reference frame (where the laws of physics don't work the same as they do everywhere else) for his views to find purchase.
Further, his writing on the topic indicates he considered Time Dilation and Length Contraction to be "merely apparent and not real", meaning that if we test for them we will always find the phenomenon empirically, but it doesn't "really happen" in the privileged frame.
His support for this is largely theological:
“We have good reasons for believing that a neo-Lorentzian theory is correct, namely the existence of God in A-theoretic time implies it, so that concerns about which version is simpler become of little moment.”
-“Time and the Metaphysics of Relativity” by William Lane Craig (pg 179).He will back that up with purely metaphysical arguments that I think you're well equipped to answer him on.
Frankly, this is the one issue that underwrites a lot of his work on the cosmological argument, so if you can attack him here, you'll be doing a great service towards undermining his arguments. You seem to be uniquely qualified to argue on these grounds, so I implore you to consider it as a line of attack.
I think this will be an exciting debate to watch, and despite what others may say, I think Dr. Carroll is uniquely positioned to do well here. I am hopeful that with some prep-time he'll be able to both make a positive case for naturalism as well as expose the unscientific assumptions Craig has to make in order to get his objections to modern cosmology off the ground.
Good luck Sean, we're cheering for you!