Hi Foxhood, you have indeed taken on an ambitious endeavour; I won't say whether it's foolish or not.

But as long as it's a project that gives you something satisfying to occupy your time with, then I personally think it's worthwhile for that reason alone.
Your list of changes at the beginning of your post are in most cases things I have thought of myself at one time or another, and I have nothing to add but that they are all very good propositions.
Here's a few comments on the rest:
Aux Output / Taigen Sound It's a bit confusing that the AVR DA names some of their timers "TCB," it might avoid confusion to refer to them as "Timer/Counter B"! But once I figured that out I understood what you're talking about. I can't see anything in your proposal that would cause a problem, other than the coding changes that will be required (but you're going to have a lot of those already anyway). The code may end up being a bit cleaner in the end, since as you say all PWM outputs will end up on the same 8-bit resolution, instead of having the Aux output be its own 10-bit outlier the way it is now (there was no special reason for that in my design, it's just what I had left).
I2CAs you've gathered, the I2C work was started with the idea of using it for barrel stabilization, as well as some driving effects. Whether those features are worth the effort I guess is up to your own preferences. I would do what interests you, and leave the rest - otherwise the work becomes a burden. I think if you were to ask the community (what five people are left

) what they'd want in a new TCB, they'd tell you things like "integrated main motor speed controls" and "integrated sounds." You could try chasing those desires, which would entail an even more ambitious redesign, but then the odds of a new board getting produced and distributed are so low, how many would profit from it? So my recommendation is to do what you are passionate about.
I admit I have grown a bit rusty as to certain details of these communication protocols, which at one time in the distant past I had at my fingertips. So I can't say whether you'd find I2C to be any less troublesome than I did, but I suspect it's possible it may still pose some challenges. Timing is important due to the incoming radio stream and the outgoing servo signals, anything that introduces delays that affect either of those will be immediately apparent to the end user as janky and erratic behavior. Maybe the TWI functionality on this new processor would work better, but I just don't know.
You could always break-out some pins for I2C/SPI and then the ports are there for some day in the future if you want to tackle the firmware side.
IR-OutI'm sure there was no particular reason why I put the pull-down in that location, I can't even be sure I had the good excuse of layout constraints (but yeah, let's assume that's what it was

). It would be better practice to put it right at the MOSFET gate, so feel free to correct that!
SmokeI agree that having dedicated heater/fan outputs is now something that would be very good, since that has become the default arrangement in the years since the TCB was first designed. I also agree that it would be fine to leave the heater output at VBat, and I doubt even Heng Long's heating elements are going to really be affected by a slightly higher voltage, it's just a wire that gets hot. But also OP Config allows the user to adjust the heat level so if it's an issue, they can just be set to something less than 100%.
As for the fan, if 6 volts has indeed become a sort of convention, then no doubt it would be ideal if it could be powered at 6 volts. Of course it's a tradeoff with extra components and board space. I'm sure the blower motors draw very little current so if you were powering that alone the 6v regulator could be very modest, probably just an LDO especially as the input and output voltage differences are going to be so small. If you decide to add servos and turret motors to the 6v rail (which is a completely reasonable idea), that could require something more substantial. If you end up needing a second SMPS and coils and all the rest, it might not be worth it to power those other actuators from 6 volts, since in the end, the servos and turret motors don't really need it.
It's been a few years since I looked at the current smoker market situation, but I seem to recall seeing them sold both in 6 and 7.4 volt versions. You will know better than me, but if they are equally as common, I suppose you could consider adding a jumper so the user could select between 6 volts (or 5 volts if you decide against a second voltage source), and VBat for the blower motor.
Anyway, these are just some thoughts, but I hope you will take your project in the direction that both pleases you best and makes the most sense to yourself.
Finally, I see you are located in the Netherlands. It could be you're just a Brit who got blown a bit eastwards, but if you really are Dutch, I absolutely have to congratulate you on your excellent (or flawless) English. Truly, bravo.