Список пониманий и функция zip ваши друзья:
>>> from __future__ import division
>>> m1 = [[1,2,3], [4,5,6], [7,8,9]]
>>> m2 = [[2,3,4], [5,6,7], [8,9,10]]
>>> [[(x+y)/2 for x,y in zip(r1, r2)] for r1, r2 in zip(m1, m2)]
[[1.5, 2.5, 3.5], [4.5, 5.5, 6.5], [7.5, 8.5, 9.5]]
Конечно, пакет numpy упрощает такие вычисления:
>>> from numpy import array
>>> m1 = array([[1,2,3], [4,5,6], [7,8,9]])
>>> m2 = array([[2,3,4], [5,6,7], [8,9,10]])
>>> (m1 + m2) / 2
array([[ 1.5, 2.5, 3.5],
[ 4.5, 5.5, 6.5],
[ 7.5, 8.5, 9.5]])