Someone would have to drastically up the tech levels for one side, for
building walkers for combat to even be feasible.

-Natsume Ranma Ranma

Okay- I've been thinking more about this, and I still 
think that a meld with super atragon might be the answer.
Brief synopsis of the super atragon elements that would 
be used-
#1 the mysterious power source found and used by the
Japanese military.
#2 the WW2 time setting
#3 the concept of the power as a test for humanity.

Eva elements used 
#1 Characters
#2 big freaking robots :)
#3 the concept of the power as a test for humanity. :)

So. we change history like this. 
	In the late 1930's a mysterious meteorite crash is 
investigated by Japanese forces in Mongolia. A supernatural 
element capable of unusually high power output is seized and
research begins immediately. Ikari Gendou is one of the men 
in charge.
	In the early 1940's Hitler's ministers begin looking for
alternate power sources for their war machines, Germany is short
on oil and this is impairing their ability to make war. Their
Japanese allies - loosing access to their raw materials in china 
share the secret element and joint research on a new weapon begins.
The Eva is developed- it is part machine, part organic (due to 
German advances in genetics) and is powered by the mystery element.
It has enormous strength and range due to its internal power 
source, and it has a force field to make it invulnerable to allied 
weapons. 
	1943- the first functional Eva (00) goes bezerk killing 
its pilot.
	1944- the allied invasion of Europe begins.
	1944- Eva 01 and 02 are ready 01 in Japan and 02 in Germany
but pilots cannot be found.
	1944- Shinji Ikari in Japan and Asuka Longley in Germany
are found to be able to pilot the new war monsters.
Asuka revels in the glory this brings her, Shinji considers it 
his duty and a way to gain his fathers approval. The Axis counter
strike begins.
	1944- a mysterious albino girl appears in Japan to warn
them that if they use the power source for destruction, so too
will they be destroyed.
	1945- The Allies finish their first weapon based on the 
mystery element- given them by powers unknown. It is called 
angel 1 - for they believe it to be their salvation....

anyway - that would be my suggestion- you could get away with 
using most of the EVA plot, but would have the conflict of Shinji
discovering that his actions could doom the human race. Also since
Japan and Germany were down to recruiting very young teenagers
by the end of the war 15 year old pilots might be believable.