This is one of the annoying things about franchise mode for me (that sometimes editing prospects feels necessary) but also one of the reasons I keep playing (because we have the freedom to fix what we don't like).
In my franchise right now, it's 2031. A good portion of MLB teams don't have a competent starting third baseman in the majors, and almost no one has a good 3B prospect. A lot of teams are forced to play guys out of position at third because the game simply hasn't generated more than a few solid prospects at that position in a decade-plus. And often the "good" prospects at third have like 50 arm strength.
Meanwhile, I just tried to trade a pretty solid LF prospect (23 years old, good defense, solid hitter, 78 overall with low-80s potential) who I figured could grow into a starter for a lot of teams in the near future. But pretty much everyone, even the worst teams in MLB, had four or five 80+ outfielders already on their major league roster. Ended up just making my outfielder a third baseman and trading him to a team who needed one.
I've edited several starting pitchers into relievers because their stamina is horrible. I've also upped stamina for pitchers. Lately I've been editing their individual pitches quite a bit, because I've found their control/break/velocity are pretty awful compared to the real players on the default roster. Seems all the top generated pitchers kinda stay with their mediocre pitch selection, and since that doesn't (to my knowledge) affect simmed games, it seems pretty fair to make some guys nastier than the game allowed.
Another thing that drove me to God mode: the huge number of mid-30s ex-major leaguers blocking prospects in the minors. I had way too many teams paying six-figure salaries to guys with no hope of ever making it back to the majors, and the actual prospects on that team weren't developing like they should because they weren't playing. Editing the age for all those guys to the max (45, I think) at the end of the season forced many into retirement, which cleared the way for a lot of prospects to finally get PT.
Really wish we had the option to add/change player-controlled teams after a franchise starts. Would make things much easier on people who occasionally want to go into God mode but didn't think 30-team control was necessary when they started the franchise.