New thought on this...
The MPEs are Adamic bodies clones from Adam itself...Could it be that Adamic souls are then the best candidates as far as functionality then? To be clear, I think that the MPEs contain the souls of the Angels. Then, since Kaworu/Adam always had a complete soul, his Dummy System could then have stronger ego, thus maintain more concentrated control of the Units as a collective as the one with the most superiority over his "children."
Granted, I'll be the first to admit that this theory does have problems...namely that the number of angels (not counting Adam and Lilith) doesn't't exactly match up...
But this kind of power over them + their souls and body types does explain their upgraded abilities - having S2 organs helps too as far as the continuous factor goes...But, then again, the angels have S2 organs as well...
It's like the MPEs are the best perfected versions of the tech Nerv was tinkering with and used in the most lethal ways..
Take for example the contrast to Unit 00
-Lilith's' soul fragment
-Adamic Body clone
-Rei Dummy Plug System
In essence, the soul/body dynamic is a kind of metaphysical body dysmorphia and the fragmenting means less ego control and over sense of instability
By contrast, all of the flaws are bypassed or overcome within the MPEs, espeiclaly if the idea of them having souls holds any water..
Although, by contrast, soul fragmenting could be what's going on here (as opposed to collecting - something SEELE already would ahem practice with in bringing Adam's soul into Kaworu's body)...They could've taken the data from what's going on with Rei or even Kyoko. The implication being the the souls are actually fragments from Kaworu following his death... I mean, while SEELE state that Adam's soul resides completely within Kaworu in the DC of ep. 24, it would seem that after he's killed, it would be fair game...Especially given the fact that we never see the MPE's until afterwards...
"Acts of Man are greater than acts of God!"
"I'm saying that I love you."
NOT FROM EVANGELION:
"You are excrement. You can change yourself into gold."