Writing this with neutrality is a wee bit easy for me ( emphasis on 'wee' ) .. since I have looked @ both DC & Marvel characters comic heroes with neutral eyes ... No !!! I am not Fibbing !!!
On an individual scale .. JLA would win easily .. with most permutations .... But considering that we are talking about Teams .... I would say Avengers would win this one ... not easily, mind you .. but win they would ...
My Reasons ....
1. ) In JLA : It's hard to ignore that there is a slight lack of mutual trust among the teammates .... probably raised high after the Batman's secret 'So-that's-my-team-member's-weakness, eh !!- ' Diary reveal . Also evident is a clash between Superman & Batman where both are so goddamn good leaders that neither would follow the other without grudge ( Superman most of the time looks at Batman as a generous elder bro giving support to a younger bro in need of help ... totally in conflict with Batman's sense of self-worth ) ... which is unlike a Tony Stark/Cap clash ( that borders on personalities & tactics .... yet there is a clear understanding on a leadership role )
2) In JLA , sure you got Batman with his Technical gizmo & gadgets ( which are awesome & excellent improvisations ) ... there isn't simply anyone like Tony Stark who is clearly an inventor of genius level ... and more importantly .. is a self-centered hero ... who often looks for an easy way out .. ( I know most heroes look at it in a negative way ... but in a battle of battles .. you gotta have someone like him in ur side . )
3) A Team consisting of A-Listers need not win the most important battle .. It;s merely the team with an 'A-list' co-ordination , trust , strategy & resourcefulness that winds the war .. and I think Avengers are ahead here.
4) Of course .. all the above points cease to exist if Superman goes mental !!
5) Also, in Avengers ... the motto is more like ' the sum of all parts is greater than the whole" ..... .. haven't got such a picture from JLA yet
My not-so-humble opinion !!! :P
Cheers for the great thread !! ..