Wren excels at quite a few things such as building a BP on the cheap, reclaiming marginal starting pitchers, making very beneficial trades, and pretty much everything to do with managing the farm system and young players. Those are VERY important skills, and I would be VERY hesitant to let those skills leave the organization.
Wren does seem to have a couple weaknesses, however. The main one is obviously the FA signing process, which could be more of an organizational problem. BJ was an overpay from the start, and I never understood why he was given so much so early in the process when guys like Pagan (my choice for CF at the time) were still on the market. Not once has Wren played the FA game of musical chairs and grabbed a bargain option at a position of need. The Braves brought in an exec this last year (name escaped me) who is probably largely responsible for the extension signings of all the young players, so it seems like the organization as a whole will look to fix this FA signing problem.
Wren's other weakness, in my opinion, is his inability to ever sell high on a player. There have been many players that were obvious sell candidates, but Wren sat on them and eventually got little or nothing out of them.
I agree that Fredi probably needs to go. Things like lineup construction may not have a huge impact, but it sets a tone. Furthermore, it is such an obvious and easy fix to not put BJ at the top of the lineup that it verges on inexcusable. This infatuation with sticking a terrible hitter in the 2 hole just to have a RHed batter between Heyward and Freeman is also nearing inexcusable. Like it's somehow better to have a .300 OBP in the 2 hole just to avoid sticking TLS there and having 3 LHers in a row?
Here's a lineup hint: if BJ or Simmons (or any6one with a sub .300 OBP) are EVER in the top half of your lineup, throw it away and try again, period. It's just so ludicrously stupid to put such terrible hitters at the top of lineup that it strongly suggests incompetence.
Another huge problem with Fredi is bench usage. For example, night game started by an opposing RHer followed by a day game vs a LHed pitcher. If you are going to rest Gattis one of those games (since he won't catch a day game after a night game), wouldn't it make sense to rest him for the night game vs the RHer so he can mash the LHer in the morning? I have never seen that type of thought put into managing the bench, and that's the kind of thing that worries me with Fredi.