Stotts may not be a good defensive coach, but he's also working with a roster that really isn't capable of good defense. Lillard and McCollum make a horrendous defensive backcourt, there's no rim protection on the team as long as Ezeli is on the shelf, Harkless and Crabbe have never been good defenders according to advanced metrics and the team's two best perimeter defenders, Turner and Aminu are only decent--not stoppers.
As long as you have that kind of personnel, no system is going to work--you can shuffle deck chairs to try and mitigate the worst problems, but good offensive teams are simply going to find the things you're trading off in your arrangement. Systems don't create talent--they enable talent. The Blazers don't have (defensive) talent.
You could point the finger at Olshey for putting together a roster that can't play defense, but his hands were tied a bit by virtue of his best players being extreme defensive minuses. Unless you're down on the drafting of Lillard and McCollum, Olshey has been in a pretty difficult predicament from the start. It's probably not impossible to build a functional defense around Lillard and McCollum (though a top-five and maybe even a top-ten defense is probably impossible), it will be very difficult while maintaining a good offense. You could fix the defense quickest by installing defensive specialists (like a Biyombo type) at the other three positions, but then the offense would grind to a halt, as Lillard and McCollum would find their air space cramped by defenses collapsing onto them. Finding good two-way players is hard enough, but what Portland really needs is solid offensive players who are defensive standouts to cover for the backcourt. Finding enough of those will take a miracle.
That's why I felt expectations for this team were too high going into this season. Portland rode a hot streak in the second half last season, and that was great. But there were clear problems that were going to prevent them from taking the next step and the likes of Turner and a rarely-present Ezeli weren't going to fix that.
In my opinion, the eventual solution will likely be to trade McCollum. As much fun as he is, especially in combination with Lillard, he's likely to be more valuable to another team that can pair him with a superior defender. I don't think it's likely that you can win with two such players, but one such can be a big asset with the right supporting cast. Trading McCollum for a good offensive player who can also play solid defense would make building the rest of the team more manageable, in my opinion.