It's so bizarre to me that people would look at the base install of essentially dotfiles as canonical and unalterable. Fork Prezto and maintain your own version.
Generally the reason to go with such a kit is so you DO NOT have to do the maintenance... you gain the benefits of the community with little to no effort.
If we were talking about a single file of up to 100 lines or so, I would agree. But presto is huge! I don't want to read the whole thing and decide what bits I do and don't want.
You're really only going after the config files, though. .zpreztorc, and if you don't like some of Sorin's aliases (rm, ls, etc) you can take them out of the utility plugin. I've spent maybe an hour "working" on my fork in the last year.