Your problem doesn't surprise me. Really, not at all. The original show has gone over Shinji with a fine-toothed comb and revealed that at the end of the day there really just isn't much to him. When he isn't being depressed or angry he easily just fades into the background because he has no other drives or quirks to hang anything on.

The 'Shinji grows a spine' thing has been done to death and never ends well. Leaving him an angsty moe blob is canon, but unsatisfying. The only solution is to force him to react to situations he can't run away from, but even then the real focus is on the problem, not him. In a nutshell, the only way to make Shinji truely interesting is to drop character somewhere and break new ground, OOC nazis be damned.