Yep, my two 50 Commandos can't really do instances.

It has made me reappraise my class make up. Now I think for PvE I will be running a Vanguard or an Assassin combined with a scoundrel. Two DPS companions and I will cover healing and tanking.

With the nerf to tank companions that becomes what is probably the only viable method to play for flashpoints. With good enough gear it might be possible to manage with two healing companions. I guess we will see.