HPTuners claims the reason we can't tune the 2.2 is the TCM/ECM link. Well the manual transmissions don't have the TCM so why can we not tune the manuals? Just something I've been thinking of.

When did they say that?

http://www.hptuners.com/forum/showthread.php?t=6128&highlight=2.2l

That seems to be the general consensus to me, that the TCM/ECU link is the hold up...maybe I'm misunderstanding what's going on.

I believe you mean the CAN network the E16 uses. The same type of network is used on other hpt supported vehicles inlcuding the already supported E67 PCM in the Cobalt 2.4L.

Isn't there still some sort of module for the transmission even if it is manual?

On the Autos there is an extra block/harness right above the ECM which is the TCM. I don't have it on mine and TCarter does.