unquestionably, Eva-01 FOLLOWING her S2 Organ upgrade became the most powerful Evangelion.
Eva-00 is just the buggy prototype.
Eva-01 can go berserk easily but that's kind of at the sacrifice of refined control.
Eva-02 is the pinnacle of standard Eva design; complete refinement of the control process, as well as fitted with *internal* weapons, etc. (I always wonder if ALL Evas can use missle-spikes or use retro-rockets, you know things that the shoulder pylons have, seeing as they are perhaps interchangeable.....nonetheless I think Eva-02 is presented as the only one DESIGNED to do that.....anyway this "refined control" goes both ways as it almost never goes berserker mode.
Eva-03 and Eva-03; okay let me simply say that "Bardiel" does not equate to "Eva-03". Hypothetically, they do not seem to be that much more of an advance over Eva-02. Practically, both of them never saw real normal usage.
As for the Mass Production Evangelions: well, lets off the bat ignore the postulation of "well, what if they had pilots in the MP Evas?" the whole point behind the MP Evas is that they DO NOT need pilots (flying is an added perk)
The MP Evas were designed so that they don't need a pilot and can thus fight until they are hamburger. It would take either A-total body dismemberment or B- destroying the S2 Engine or Dummy Plug, to deactivate an MP Eva.
The drawback of course, is that they're morons: they're just animals, they're not as smart as a human pilot. I mean they outnumber Asuka 9 to 1, but they proceed to attack her ONE AT A TIME instead of trying any coordinated battle plans WHATSOEVER. Of course, they've got replica Lances of Longinus, but that's not an "Eva" feature that's a weapon, and Eva-02 could have used it just as much.
Long story short: Eva-01 POST-Zeruel, with and S2 Organ, vs the MP Evas? Well in actual EoE, Shinji didn't even get a chance to fight them because 3rd Impact began.
However....ultimately due to Eva-01's use of a living pilot and capacity for creative thought as a result, I think it would outperform the autonomous but stupid MP Evas.
As for Eva-01 PRE-Zeruel, this is all debateable.
Eva-01 and Eva-02 (before episode 19) are just so evenly matched; Eva-01 is a bit more berserk and its an experimental "dead end" with Lilith they tried only once, but Eva-02 is the Production Model that they really refined a lot. So really there is no clear favorite.