Needing to verify predates Creo. It is part of Intralink/PDMLink integration in order to make certain that parameters in the instances are correctly calculated so that they appear correctly in Intralink/PDMLink. I haven't worked outside a pdm system for a while, so I don't know if the verification is required there, but there is a verify-on-save option to make it automatic with saving.
What's the dislike about the files? Disk space is pretty cheap, though large numbers of files do require more time for making backups. As mentioned, the reason for the increments is to act as a safety net against file failures or user errors. I've seen users delete all the older versions, only to discover the latest one is corrupt, which you don't discover until it's been opened again.
If you often want to purge older files, look into creating a script that runs when you start Pro/E or prompts you to run when you start as a reminder.