My view on this is that Mxy has always been a joke character. With all his power, he has been defeated time and time again by rather small fish (by comparison anyway).
Even EJ was basically defeated by believing that he didn't have control, and thus he lost control.
More over, his feats, while impressive, from what I recall, mostly altered earth and its reality. Sure the effect had a cosmic impact, but he never ventured beyond effecting earth's reality.
Thanos with the IG took on everyone and everything on a cosmic scale. He only lost because he chose to limit himself and paid for it in the end. If he had not put the restrictions on himself, he was all but unstoppable.
Judging from the feats I've seen them do, I give this one to Thanos.
And I'm choosing to ignore the dumb idea that Mxy can enter our reality and change what the writers write. First because this isn't Mxy we are talking about, this is EJ. Second, it was a one time thing that the writers threw in there just for fun. Sure, you can even argue that it's in character for him to do this, but I doubt they did it with the intent of implying that now Mxy was all powerful and completely untouchable by anyone in the DC, or any other universe for that matter. If he could do that all the time, he would've never lost and things in the DC world wouldn't happen without him giving it his okay....Then again, maybe that's what's been happening all along. This could explain a lot of the bad writing that has happened in the past... 😛