I like the idea of Lazard being a main villain. They've already got a moral conflict there, and I think it would incite a lot of psychological warfare within Zack. An underlying theme in which people with different motives work with/under each other and get themselves into unfortunate situations wherein they question their relationship with the people they work with and their purpose in life. Though I'm considering how this would fare for the progression of the plot and Zack's motivations; the copies were a plot device that served as a concrete/undeniable antagonistic group to Shinra and to global security. Perhaps dump Genesis completely (I personally think two major Jenova products, namely Sephiroth and Angeal, are enough, for the sake of maintaining the 'snowflake' status) and utilize AVALANCHE again (who were incidentally not even mentioned IIRC despite the game overlapping chronologically with BC). I personally thought Angeal had a lot of potential; I like the idea of a father figure to Zack (and a sole friend to Sephiroth) that manifests itself within Zack and Cloud's relationship later on and embodied within the buster sword. Additionally, he would serve as a nice bridge between the two parties (Seph and Zack). Keep Hollander, too. Lots of characters I think are a good thing because the original game didn't really capture at all how huge Shinra really is. 2 dimentionals are fine imho as long as they don't take the spotlight.
In spite of an earlier post, I must say that I actually thoroughly enjoyed the soundtrack; I felt it was different enough to establish it as a different game but still retained the original spirit and threw in some decent renditions of classic tracks. I also approve of the usage of the same menu soundbytes in series games; it's subtle but it really does add a level of continuity.
My gameplay complaint - make Hollander a less tedious boss. Add another mode between easy and hard. I thought the Materia Fusion was pretty cool since it satisfied my customization fix; generally stuck with Dark Firaga, Osmose, Curaga, Steal, etc etc, beefed up with stat buffers. Didn't find myself using Command Materia often.