Boy do I feel your pain! I have driven manual trans trucks until my 2010. If there was one thing I could change about my truck, it's that!
My previous truck was an 08 hemi with a 6 spd, and it was the only manual trans hemi my dealer had sold since may previous truck....04 hemi with a 5 spd.
It may be a simple 'supply/demand' thing. As most people obviously don't want the manual trans, they have just quit offering them.....too bad.....I really miss my manual.