You're overlooking the critical fact that all members of SOLDIER are Sephiroth Clones, as well as the fact that Sephiroth easily defeated Zack (prior to Zack's captivity).

Moreover, given the nature (always living, even when divided) of JENOVA cells, any advantages and/or disadvantages should have vanished when they were purged. They were irrelevant to Cloud's power, really, as his abilities are essentially the physical embodiment of his extremely strong Spirit Energy.