Both use the bitcoin block chain so confirm times are the same.
There are no new coins of either.  There are more Mastercoin than Counterparty
Since they are on the bitcoin block chain, they use the same algorithms of bitcoin, they are not separately mined, or merge mined, they use the bitcoin protocol as the fundamental layer.

The feature sets are fairly similar, the implementations have significant differences.  Both of these change rapidly though as they are under heavy development.