Here's how you incorporate the sky blue/white, red rose, 3 rivers, a nod to St.Marks, some of the CoA colour scheme and the Manchester bee (colour scheme):
...And here's a modern, predominately sky blue/white alternative in keeping with the current badge's colour scheme of the rivers:
Sorry if my image editing skills (of GeekinGav's original design) make you feel inadequate about yourself ;)
I'd be happy with a professional's tidier version of the second one, I think it incorporates everything important about the club's history and Manchester without going over the top. I think a black ship is a class thing to include to represent the original version of the club and original kit - plus it doubles as a silhouette style. Looking at the top one - I'd thought about including more black to represent St.Marks but after seeing it, that would likely encourage Nike to give us sky blue/black strips rather than sky blue/white like we should be.