There's that too. Unit 01 has been tampered with and had a human injected into its core. Unit 13 was built after 14 years of Eva-on-Eva war for a particular task and seems like it's specially designed to counter what Wille will throw at it. Wille's Evas have limited battery life? We'll arm it with a barrier to stall for time. They have Anti-ATF ammo? The Eva doesn't have one!
Maybe Unit 01 isn't supposed to have an ATF, or Unit 13 is and Seele used some arcane shenanigans to get rid of it. Neither one is solid evidence for what an Adam "should" be on its own and the movie isn't even clear if Unit 13 can neutralize an ATF with whatever it has. Mark.06 probably has that answer and the stupid thing went and got itself killed.
The (non-canon of course) pachinko games play it both ways. Some times it can do all the crazy rocket punching Unit 01 does and sometimes it can't.
Sachi: That's what I think too.
Gendo is very good at playing the subservient lapdog and Seele thinks they've taken away all his toys and broken him to their will. They die thinking everything has gone to plan, apparently without realizing that Gendo has boned their whole team and is about to take their Eva. Shinji might have been their last insurance policy against him.
Someday I hope that we'll be reunited if that is what's destined to be. Perhaps we'll discover that elusive bible. And then we will finally be free!