I am sure people have stated various reasons why CC should be integrated into iClone as opposed to having, for the most part, independent software.
Here are a couple of issues that I observed:

1. File Format Duality

iClone and CC don't share the same file format for some of their files. For example, there is iCloth vs ccCloth or iAcc vs ccAcc. While switching between the two formats is fairly trivial (load them in the other software and save them), it creates problems for the Marketplace. Marketplace allows content to be associated with one software or the other and no matter which you choose, your potentially losing out on some customers. Some user like to dress up characters fully in CC and then push them to iClone for animation only. Other users like to use CC to make a bare bones character and then add accessories (or even clothing) in iC7. This means if you don't create 2 version of the content, one for CC and one for iC7, you may miss some potential CC user if deploying as iC7 content or miss some potential iC7 users if depolying as CC content.

If we had one standardized set of file formats (i.e. if iC7 and CC used the same clothing and accessory files) then this problem would be eliminated.

2. Render Engine Discrepancies

If CC was part of iC7 then both software would use the same render engine eliminating discrepancies between the two. As it is now, it seems that iC7 and CC don't use the same render engine code which causes discrepancies between the two software. For example, I created some custom clothing in CC. I adjusted it so that I had no peek through in CC. Then I pushed the CC character to iC7. Without even changing the pose, the CC character arrived in iC7 with poke through. Thus i had to go back to CC, overcompensate the peek-through adjustment (guessing since it looked okay in CC) and then re-push to iC7. Not a big issue but it shows that the two software do not use the exact same render engine code.

"We often compare ourselves to the U.S. and often they come out the best, but they only have the right to bear arms while we have the right to bare breasts"
Bowser and Blue, Busting The Breast