I'd have to says autos cost more to fix. More complex and rebuilds sometimes go awry...
Manuals seem to take alot of abuse...from what i've seen / read.

On the other hand -
On the Supra TT - they come in auto or manual. The auto is good for under 500. The manual on the other hand is damn near bullitt proof. Ryan Woon hits 8 secs. i believe. Granted the manual is manufactured by Getrag.

Cost to fix :
Auto - cheap b/c you can find another used one for less than rebuild cost under, $500 back on the road.
Manual - expensive. rebuild approaches 1 - 3K depending on what u need. (Also not anyone can rebuild getrag for TT and get it right) New $5k - $6k from dealer. Also, so many people are doing manual swap thus keeping used prices up. $2k min for one, used.