I’d change every hole on Black if we were talking about mowing lines.
While it might be a maintenance issue, I'm still interested in the detail of what you're getting at, specifically on...
2, 5, 9, 12, 15... ?
There probably are few courses as good as Bethpage that suffer so adversely from overly-narrowed fairways and thick rough, robbing much of the original strategic intention. It's terrific challenge comes from the land movement, bunkering and length. It doesn't need more defense, unless it's being set up purely for modern major championships — which it is, sadly.
Of the holes you mentioned, I'd say only #9 is set up well, assuming we ignore the greenside bunkers being buried in rough. #2 is the only relative short par 4, so even though the fairway is needlessly narrowed, I could give that a pass for now.
But #5 is egregious. Like most holes on the course, the only option off the tee is long and straight over the bunker with no truly safe lay-up option. There is an ocean of unnecessary rough on the left side of the fairway that should be short grass, tempting players to hit out in that direction and leave themselves with a much tougher approach that could be longer, blinder, blocked out by trees, with more carry required and with a harsher angle for bailing out up by the green.
It's the same issue that's found on #15. Oceans of open rough surrounding U.S. Open-narrow fairways. Both holes are already the hardest on the course, requiring your longest, straightest drive of the day, and then both have the two uphill, all carry, long approaches that help make the course famous. You could remove all the rough on #15 and it wouldn't play that much easier. Without a perfect long drive, that second shot is one of the hardest around even from short grass. Even worse, the slight left dog leg effectively narrows the landing zone even more off the tee.
On #15, the right side fairway should be well-expanded. Players should be tempted to play safe out in that direction, setting up a similar situation as #5. It leads to a longer approach from a worse angle with more carry and less bailout by the green. My preferred miss on #15 is the left rough, cutting the corner a bit and having a strip of un-bunkered grass directly between me and the green to bailout short on.
#12 is similar again. The fairway is blind, with a slight left dogleg, and the safe play appears to be out to the right where you can see some landing area and a lot of open space. But the fairway is so narrow that most shots in that direction roll through into the rough, compounding what is already a longer second shot and worsening angle to the green. Players should be tempted to play far out right, especially if they aren't confident clearing the fairway cross bunker. As it is, thanks to the uber-slim margin of error like on #15, the only drive that works is perfect and straight or perfect with a slight draw.
And don't even get me started on all the rough down the right on #6, removing probably the best strategic decision on the course: playing the straight hero shot for a clear look at the green, or playing out safely right and having a blind second.
It's frustrating because you could remove all the rough on Black and have one of the most fun courses you ever played. The only thing the current set up has going for it is that you get to see how many times in a round you can pull off the exact perfect drive you envisioned in your mind, because anything less is usually in extremely boring rough trouble. But that's the point. The tourists want to get their butt kicked just like the pros did in '02 and '09. Meanwhile, us regulars only get part of what is otherwise a truly special course.