Here are the quick fixes that would be helpful prior to a potential re-write (or edit) of the simulation algorithm.
1. Roster validation tool for commissioners
Allow the commissioner to mark each roster as verified, and have it reset to unverified if the owner pulls their team and then re-enters. You currently have to track this outside of WIS, and there's no way to know if someone you've already verified has made changes and then come back.
2. Make a note in the league chat every time the commissioner uses the Replace Player tool
This is currently ripe for abuse. I have no suspicions against any individual, but seeing how it functions now an unscrupulous commissioner could very easily cheat. If there was an entry in the league chat saying "Commissioner replaced Player X with Player Y" every time it was used that would squelch this possibility.
3. Hide names of sim-generated AAA before the schedule is generated
Also ripe for abuse. Simple fix.
4. Progressive Draft Tool
Like frazzman said. A tool that allows anyone to pull a list of all players for a given season or range of seasons, sorted by position then by last name. Add a window to the tool where you can paste in keepers and then those players are automatically removed from that list. Also allow filters by first and last season to pull rookies.
I have opinions on how the sim could be improved like everyone else, but reasonable people I think will disagree on how best to implement those improvements, so I would suggest in the short term we focus on quick, relatively easy and non-controversial fixes like these. If new ownership is responsive and willing to make huge engine re-writes I'm all for that, but a few quick wins like this would be great.