In terms of performance during the series, 01 by far. However, it seems like 02 had many armament improvements (and perhaps performance upgrades?). 03 is an unknown because his properties seem to have come from Bardiel, and 04 is a complete unknown. The MP Evas would be the pinnacle, I suppose.
As for destroying MP eva brain matter, it doesnt work- Asuka explodes the heads of three (?) of the MP evas, and they come back despite their wounds.
As for the wings, I suppose long training would lead to the pilot learning how to fly. In that sense, it would almost be like the reverse of a ghost limb; you are learning the sensation for a non-existent organ rather than having the feelings for an organ that once existed.
The unlimited power supply is kinda stupid, since it seems that all EVAs can go berserk, which makes the S2 less important (01's ingestion of an S2 makes it even less so). I still say 01, simply because Yui's soul was the most...powerful? dedicated? Regardless, she had the best performance