NXE's a pretty decent treatment of the "so let's have someone who isn't a spineless wuss hop in the Eva and kick ass" flavor of Eva-fic in my mind because it doesn't succumb to some of the worst sins of the 'fix-fic' genre. Shinji isn't retroactively changed into some kind of ass-whupping gang leader, and by extension the other characters remain similarly true to their original sources and still react in-character to the situation, albeit a changed situation brought out by canon-brazing* of X-Com by way of DJ Croft as a brazing rod.

Mixed metallurgical metaphors aside, the only real quibble I have with the story is--and I'm going to assume that 'spoilers' are somewhat irrelevant in this context--Gendo's snap-back from mind control is, in my recollection, a bit on the erratic side. Granted, I imagine that's at least partly the point, but the whole business where coldly-logical calculating Gendo turning into a manic cheerful pixie (and getting his old clearances back without supervision?!) kinda throws me for a loop.

The presence of DJ (And, by extension, Lara, the X-files refs, X-COM, etc.) really doesn't break nor weaken the concept, as they enable the work to expand without compromising the character of the Eva-canon characters. This is something that's lost in those fics that change Shinji's essential character away from an ignored, unwanted child with all the mental issues that entails.

* If canon welding is when an author takes two previously discontinuous continuities of his own work to weld together into a single piece, then brazing--the joining of different metals--would be the logical phrase for taking discontinuous authors and joining their works. Yes. I am far too into metallurgy recently. I have a ball-peen hammer now and I am -happy-.