A few thoughts:
1. The 12.5" Baer kit DOES NOT fit under the slicers. It will fit under many (maybe most) 16" aftermarket rims, but not under slicers. The 12.2" kit _barely_ fits under slicers, and then only with a spacer. Many people find 16" rims favorable for road course use since they do provide some handling and tuning advantages. Usually the motivation for getting bigger rims is to fit bigger brakes underneath them, but, as mentioned, there's not going to be much performance difference between the 12.5" and 13" systems for these cars. I opted for the 12.5" because it was close enough to the biggest system and still allowed the use of 16" rims.
2. Bigger brakes (i.e., larger diameter rotors) provide more braking torque for the same clamping force. The larger rotor can absorb a bit more heat, but that doesn't really help much. Directional vanes and larger area do help ventilation and radiative cooling.
3. The 2-piston PBR calipers provide better brake modulation. Once you get used to multi-piston calipers, single-piston calipers seem crude in comparison, especially in brake release. Since these calipers are aluminum they're also lighter and dissipate heat more easily than the stock iron calipers.
4. ABS is not a limiting factor in braking performance. If you're doing things right, the ABS should never (or at least seldom) kick in. Threshold braking will always result in shorter stopping distances than if the ABS is pulsing the brakes. If the ABS is kicking in during braking, especially in the front, that's a signal that you're applying the brakes too quickly (rather than squeezing them on) or too hard. Race rubber helps alleviate this as well since the tires won't be as apt to slide. If the tires are sliding easily bigger brakes won't help; it's good to try to match the tire and brake effectiveness so that you don't have too much brake for the tire or vice-versa.
5. The only way to completely eliminate fade at the track is to keep your foot off the brake. Plenty of people have melted down every possible brake kit for the SHO because it's not hard to do. The SHO is a fairly heavy car capable of some pretty decent straight-line speeds, so it's not hard to cook the brakes on a road course, especially if the course layout is ******* brakes. I've got 12.5" Baers, TCE two-piece rotors, Porterfield R-4 pads, 3" ventilation ducts, and Castrol SRF brake fluid, and if I over use those dudes I can still melt 'em down in a hurry, especially at AMP (which is ******* brakes). The mod that had the biggest effect on brake management for me was the ducts.
6. The point of going to bigger brakes is to a) shorten stopping distances, especially with race rubber, b) increase the heat tolerance of the system (i.e., have something that can handle more heat before failing...not immune from failure, just an increased failure threshold).
7. Pads make a huge difference, too. There are lots of tradeoffs, though, especially between grip and rotor wear.
When I first started tracking the SHO with the stock brakes I learned very quickly that I had to leave a fair amount of room between me and the Porsches/BMWs when entering a corner or I was going to leave a big imprint in their rear bumper. I was lucky to learn this without actually hitting anybody. Once I got the Baers on with track pads I could brake with those guys easily for a few laps, then I had to back off. Once I got the ducts and the SRF in I could brake with them (even outbrake them sometimes) consistently throughout a session, as along as I'm reasonably careful to manage them.
Good brakes make a big difference. It took me a long time and a lot of patience and development to get a system that works well and consistently for me. Technique matters and other folks have worse/less problems that I've had. Lance still uses the 96 brakes with the stock calipers and does really well with them (but his car is reasonably light, too).
Jedhead - I'm glad to see that you and the other folks that are getting Todd's two piece rotors for the 12.5" kits are benefitting from that work. You're all most welcome...Todd makes good stuff.