What to do? Weak Dot Com or Strong Dot Net ?

Ive a 17 year old Dot Com keyword domain that got hit with the EMD update and fell out of top five for its keyword.
Rankings Doesn't seem to be coming back, Ive accquired the Dot Net of the same keyword which ranks better than the Dot Com and has way more backlinks and is nearly as old.

Now just wondering should I keep both sites going as separate sites? or redirect the dot com onto the dot net ?
Ideally I would like the dot com site on the dot net domain but I would hate to have to do 301 redirects for all the old content on the dot net as there is thousands of pages on it.

So if you got the dot net and it was stronger and ranking better than your dot com that got hit with the EMD what would the best way forward be?

Actually it's well knows the EMD wasn't a punich for EMD sites. They just lowered the importance of EMD in Ranking. So that the sites that depends on EMD to rank with low quality content ...etc would get hit

You say you got thousands of pages on your .com sites which is weird for me ! or are they garbage content ! if not then the EMD wouldn't affect you like that ! Something is missing here.

The dot net has thousands of pages not the dot com.
I would guess the quality of the content of the dot com is weak but was good enough to rank top 5 for over a year.
The EMD update also coincided with me changing theme and server which probably didnt help matters.
There is no manual penalty according to webmaster tools on the dot com.

The Dot Net ranks top 5 with many number 1 positions and would get 10 times more traffic than the dot com.
My main question is do I run them as separate sites or merge them together?

.net provides better redirection. So, I think you better to try that.

Build some quality links to the .com and see if that improves the ranking.

Leave it as it is