Imo, the only things to fix in LFS transmission modeling are:
1. Proper ignition cut. The way Scawen has currently coded it is wrong and slow, the ignition cut doesn't mean killing the ignition of the whole engine (and I'm pretty sure it does just that, although then turbo boost would be dependant only on throttle pedal position). In real life it's enough to cut the ignition on only 2-3 cylinders of the 6 or 8 cylinders in the engine, just enough to unload the transmission and enable the dogs to catch next gear. This is why XRR is still slower than FZR in accelerations, too much time lost with the current ignition cut (it'd be much faster to just give it the regular lift-type sequential, and yes, it would outweigh any disadvantages of losing some boost for a split second).
2. Having the option of autoclutch only on downshifts in cars with sequential gearboxes (ign. cut and regular), because that's how shifting is done in 98 % of the cases of dog-boxes in real life, making it a lot easier to blip the throttle (without chancing a miss-shift or riding the throttle as many idiots do).
3. Gearbox damage. Stresses on gear teeth and dog rings can be calculated pretty easily and a wear model could be introduced, this would be especially handy in endurance racing and it would force people to learn how to take care of their cars (and not skip blipping the throttle).
4. Clutch heating/wearing model re-done. Currently you can still flatshift in a 500 hp car during the whole 1-hour stint and not have your clutch temp go into the red area, and this is ok, racing clutches made of C/SiC don't really care about being slipped or their temperature, but what they do care about is being constantly stressed with impulses during flatshifts (and not only the clutch, but the whole drivetrain). This is another area where a vibration/stress model would be benefitial (especially for flatshifting in road cars).
5. As yaper said above, dog H boxes on racy slower cars (FWD GTR, FZR). Maybe even a DSG transmission for the never-coming Scirocco.