I just bought an LMT Defender lower with the fixed A2 buttstock. I want to put an A2 upper on it; probably a full-sized upper with 20" barrel. What is the best I can do? I was thinking about trying to mate a Colt upper, but I understand that Colt uses different sized pin holes. Is this a problem. Also, what is the best mid-length upper available? I see that RRA makes them, but I want something better (ala Colt, LMT). I want this thing to have the fixed handle and the traditional handguard, but be of the absolute best quality. Any advice would be greatly appreciated. Thank you.
If you want an A2, I’d say go for an A2 upper.
Fidelis Firearms has this listed:
M16A2 Upper Receiver
The whole page is here
I have never bought from them, so I am not endorsing them per se.
I believe that it accepts the normal takedown pin size.
Thank you. 
I would pick up a Sabre Defence Mid-Length upper from PK Firearms w/out the bolt, and put an LMT bolt in it. 
Is Sabre as good as Colt or LMT?
I have made a few purchases from Rod before and would recommend him.
I would also suggest the Colt M16A2 upper half they have small pivot pin size and sometimes I put my Colt M16A2 upper on my LMT Defender lower without any problems.
My M16A2 upper is usually on it’s own Colt Match Target HBAR A2 current model lower with also small size pivot pin.
If you would like to get a high quality midlength gas system upper take a look at Noveske.
Does this mean that
sometimes there are problems?
or
sometimes you swap it around?
Sometimes I swap them around.
M16A2 upper on LMT lower, sometimes my LMT 16" m4 upper on Colt 6721 lower, sometimes M16A2 upper on Colt 6721 lower, etc., if the uppers and lowers are in spec there should be no problems swapping them around.