Grasshopper-san pretty much clarified why the the TF and Eva concepts dont really work well together. Evangelion operate using an external power supply that looks like a giant power plug attached to the Eva., once severed their internal power supply they can operate for 5 minutes. Transformers operate using energon and free to la-di-da for longer periods. The way to combat an angel is to process an AT field which I think cancels an opponent angel's AT field at close combat. This would have to suggest if Transformers are to fight the angels they would have to an angels themselves

The two series are quite different in terms of violence and realism. In the TF cartoon and comics you don't see dead bodies and graphic violence. Things are rarely destroyed and there is not much tactical strategy in fighting. Eva. is definitely for a mature audiences and there definitely alot of adult themes.
Transformers I think could work out as supporting units for NERV to fight the angels. We usually see tanks/aircraft getting one shot so TFs should stand up to some punishment.

I think this is a great opportunity for something big, I love how many different stories are told in the franchise, there is something for everyone's' taste.

I wrote something about it here
http://burntrolls.blogspot.com.au/20...lt-is-not.html