Your Avid MC purchase probably included Sorenson Squeeze. Send your sequence to it and try one of the H264 presets there. You should be able to get it compressed more efficiently , and with better quality than a direct Avid export.
MKV is actually a container (just like QuickTime). In many cases, the file compression is H264 as well. Though it is actually pretty cool, I think the general public is fairly clueless about it and it will end up causing you grief if you use it.