Hi there
I haven't got the E12A but I do have the Fiio E12, so I can make some comparisons there.
It is early days with the NX3 but I can definitely say that the NX3 has a MUCH wider soundstage with instruments placed well within that sound stage with good depth. The E12 soundstage is good and I enjoy listening to it, but there is no doubt that the NX3 wins hands down here.
Both the E12 and the NX3 are warmish sounding amplifiers. Both sound very good.
I would say that the NX3 has some warmth at the lower end (without bass boost) and perhaps is a tad less smooth at the top end, but it is still burning in.
I think the bass boost is better on the E12, the bass boost on the NX3 is muddy and not needed as normal mode has lots of bottom end. YMMV.
I think though for it's price point is a very good amplifier - probably the best amplifier in this price range. I also have the Fiio A3 and there is absolutely no doubt in my mind that this mplifier is better than the A3.
I would say the NX3 would be a great match for anyone who has slightly bright headphones that could do with some warming up and need some weight at the bottom end. If your headphones are already strong in that region they would probably pair better with the NX1 that adds the airy top end. (I still think the NX3 has plenty of air though).
Hope this helps.
cheers
John