This post is for D3 only. I have no experience running a zone above D3 but I have over 30 seasons of D3 experience running a zone.
My opinion is that it is still quite possible to win with a zone. I recently won two national D3 titles running zone. So it would be hard for me to argue otherwise. (Granted it's Phelan so a national title in that D3 world is kind of the equivalent of winning a good conference's tournament in a normal world.)
That said, I'm of the personal belief that potential did a lot to hurt the zone defense. And I'm not sure the fact that I ran a zone did anything to help with my good run. In fact, I feel pretty strongly that had I been running either a man defense or especially a press I would have had a much better team. I won because the Phelan world was completely bare and those teams that did exist had such a high level of coaching turnover that it was pretty easily to build a team that was head and shoulders above the rest.
I wouldn't go so far as to say I won in spite of the zone but ... well now that I type that ... I actually do think I won in spite of the zone.
Playing a 2-3 zone is supposed to allow for the following advantages:
1. You can get away a bit more with bad defenders in that the ratings are averaged across the board. That might mean plain mediocre but that's better than bad and tougher to exploit.
2. It's possible to completely ignore defense for all 5 positions and still be fairly successful at the D3 level.
3. Players foul less often.
4. Stamina is less a factor
5. I think a doubleteam is best running using a box and one compared to a man defense.
There is still a place in this game for bad defenders and/or ignoring defense. But prior to the potential there was a lot more room for those players in my opinion. Footwork practice led to very modest gains in defense and there was a lot to the fact that you recruited for defense while you developed the other categories. Now with potential, the rate of improvement is the same and the penalty is that much higher if you ignore the category. So you can still run a zone, but the benefits of doing so are a bit weaker.
And I personally felt that the biggest advantage to the zone prior to potential was the fatigue factor. And this advantage was actually heightened in that brief period between the "fix" to the press and potential being implemented. You needed to have a full team of above average stamina players to play the press and you could punish a press team by going uptempo with a zone defense knowing that your zone players aren't getting nearly as tired as those playing the press. But now with potential, it's a snap to get a team full of players with stamina above 90, with several at 99. When the press teams have stamina that high, the zone can't punish them. There's still an advantage of course, but one that is much more difficult to actually exploit.
And while it is still an advantage that the zone causes less fouls, potential has made it extremely difficult to have an outstanding free throw shooting team. Even here potential has minimized the impact of how the zone can help a team out.
So of those five advantages above, four of them are diminished with the potential and the other is the doubleteam advantage that I'd argue is a minimal benefit to the zone at best and those benefits don't come close to those possible in the man or press. Does this prevent a team from winning with a zone? No, the more talented team is typically going to still win. But if you took otherwise equal teams and had them face off against each other running different defenses, I really don't think the zone comes close to winning half the matchups.
Right now the zone gives up the worst FG%, creates the least amount of turnovers, and gives up a high percentage of offensive rebounds to the opponent. That used to be somewhat balanced by the things that you'd gain. But those benefits have been greatly tempered in my opinion and I don't think the disadvantages are any less today than they were a year ago.
Again, this isn't to say you can't win with the zone. The disadvantages to it aren't nearly enough to have lesser teams pull upsets over a better zone team all that often. But you are sort of playing with one hand tied behind your back. Well maybe not one hand since the disadvantage isn't all that strong, but maybe a finger or two.