I agree about prechecks especially when there's rpm managers available to check if things are installed or not as well. Though I roll my own apache and php from time to time and rpm managers can't handle those.
I know it wouldn't be an easy task but could be an gradual improvement.
Another annoying issue is the upgrades where certs are already configured yet the upgrade wants to redo them. I usually back them up and enter garbage to get past them quickly but I think the best solution is to build certs using "ispconfig.crt" and "ispconfig.key" and when the upgrade occurs, it check if these files exist which would then bypass as they are ISP related certificates.