I think that with respect to well rounded cars like ours, manual transmissions will always be more popular. Indeed Porsche sell three manual equipped cars for every Tiptronic that goes out the door--and that includes all of their tiptronic-only SUV's.
I think a better question with respect to the pro-touring formula would be:

How valuable is overdrive for a pro-touring car?

Whereas overdrive (either manual or auto) allows for transmission gear ratios that are far more appropriate for a well rounded car. Overdrive allows for a steeper 1st gear and better 2-3 gear ratios. Which combined with a middle of the road final gear ratio (3.50:1), works best with our relatively short rear tire diameters for excellent straight line acceleration. On the other end of the equation, an overdriven high gear provides better fuel economy and higher top speed. Performance nirvana.

I always found my TH350 / 3.90 / 275/40ZR17 combination to be somewhat dissappointing. In fact, I'm bummed that PHR selected a TH350 for G/28. I understand that cost is an issue, but a built 200-4R or bone stock junkyard 4L80E would have better fit the performance goals without breaking the bank. We can argue price all day long, but balance price with performace goals and I know I'm right. (I didn't get very far arguing the point with Johnny, though)

So Bringemout
If a TH400 is in your future, I recommend backing it up with a Ford 9" so that you can try different final drive ratios until you're happy. When in doubt, a 3.42 or even 3.31 will maximize all around performance at the expense of E.T.
Even then, when the road gets curvy, or if you find some room for high speed testing, ;) you may find that the 3 speed trans is holding you back.

Roger that Streetfytr, thanks for the input. I appreciate it. As far as the gears, I was wondering about a good gear for the rear end, 3.55? 4.10? ya know??

For a TH400? For best all around performance, I would go the other way because top speed and highway cruising are bigger priorities
With a 4L80 the choices are wide open

Here: Mess around with a gear/mph calculator.
http://www.f-body.org/gears/

And Gear Ratios can be found here
http://www.tciauto.com/tech_info/gear_ratios.htm

actually.. soon it will be

6L80+paddle shifter > 4L80e+paddle shifter > *

:)

A manual is NOT required.. although my current ride will have one just to be different from my last car..

I just read that 6L80 article in Hot Rod. Sixth gear is .67. Isn't that the same as the 4L80 or close to it? I guess what would be the benefits besides being able to handle more torque and having 5-6 chirps in the back?

I'm still stuck on liking less gears... I HATE hearing my engine/tranny having to struggle through 6 gears in every day traffic. My car has enough jam to just pull in the gear its in, or one kick down. Not to mention having to row through 6 gears(in a manual) vs 4/5

4l80>6l80 for me.

-Matt

Steve C will your paddle shifter work with the new 6L80E????? I am assuming it will....but just asking!

Steve R when will this trans be released? have you heard

You will be waiting a long time to see a 6L80 in the aftermarket....Clutch to Clutch trans vs. a Step Gear 4L80E.....

My paddle shifter is essentially just an electric actuator. So the answer should be yes. A better question is: What will it take to adapt the 6L80E's sophisticated electronics to a hot rod. According to my source, that adaptation will be a long time coming. If possible, it may require scrapping the OE computer which would be a shame.

As for the 6L80E having too many gears, I don't think that's how it works. At any given time, these modern 6, or 7 speeds can be looked at as multiple four speeds in one. The computer decides which of the 6 or 7 available gears are appropriate and omits the rest. They just have a more diverse menu of ratios to choose from--kinda like a chinese menu. You wouldn't dare order one of every item offered by China Delight, but somehow, any dish is available when you ask for it.
With the Mercedes 7G 7 speed transmission, the computer might launch in second or downshift from 5th to 3rd without passing thru 4th.
So from point A to point B, that 7 speed might only use four gears-maybe not. Which four is up to the computer. When sequential gear changes fo occur, the close ratios allow for very smooth shifts.

keep in mind...most poncho motors are "grunt" motors, they tend to like a lil less gear. again it really depends on your driving habbits.... but i would say 3:30-3:50 with non-overdrive trans.