This is ofcourse a non-question. Neither is correct, both are valid answers.
Method two however weights it by larger numbers which in most scenarios is probably not what you want. The relationship between A1 and B1 is mostlikely as important as the relationship between A3 and B3, even if A3 is ten times teh size of A1.
For my work, I need to use method one and average all the divisions, rather than summing top and bottom.