I think the problem here is in the unexpressed thought that every hole need have every stroke made on it be a challenging one. Why is this a requirement in the creation of a three-shotter that is able to challenge the accomplished player while it remains fun to play for the average one?
Here are two examples that fly in the face of this supposition, are quite different from each other, and which have, when the individual strokes are made well, at least one expected stroke that simply is not a major challenge. Both are on the same course yet are decidedly different in length, challenges offered, lay of the land and design.
The 4th hole at Bethpage Black is near-unanimously considered as one of the great par-fives on the planet. At 540 yards it is not overly long and theoretically should be reachable by good players in two shots, yet in the Open championship in 2002 not a single eagle was made on the hole by someone who reached the green in two and there but a handful made in 2009, and these are/were the best players in the world competing. For the very accomplished players a step below that level, the drive is not particularly daunting, but unless the approach shot is perfect one will be left with a long wedge that must carry a large area of rough and big, deep bunkers to a green that runs downhill and away from you, and that even if it is in the fairway. if it is struck even a bit wrong then it will find itself in deep rough and maybe even one of those bunkers. It takes two very good plays to leave oneself the easy third shot from directly right of the green, and even that is no gimme' as the slope of the green must be read well to get the pitch shot close.
A not difficult drive and a somewhat easy pitch and it is still one of the great holes in the world by anyone's standards and a wonderful challenge regardless of one's skill level.
The 13th hole on Bethpage Black. Again, here is a hole that also didn't give up a single eagle in 2002 from someone who reached the green in two and again, only a handful of them in 2009. Whether played from the front tees at 535 yards, the old back tees at 586 or the new championship tee at 640-660, this hole is not as much about length asn it is accuracy and risk/reward choices. The drive's landing area, even with the course set at "U.S. Open" widths is generously wide for even an average player. It is, once again the challenge if the second shot, that also sets this hole apart from Mike's theory. Even the big hitters have a go/no-go decision to make depending upon their drive, and often it is a dual one. For there are two potential lay-up areas to consider depending upon how the drive ended up. The large bunker on the left side that both protrudes into the fairway as rises up and out of the deep swale in the land also narrows down the landing area before and after it causing one who has any doubt of carrying it to lay up well shoprt of it, leaving a 170-190 yard third shot. If they try to carry it, they also need to be very accurate because the fairway, which is very narrow here, runs away at a slight angle making it effectively a much smaller target to hit. The big hitters who choose to take a run at it int wo face the large fairway bunker that must be carried on the fly. If the shot does so and is even a bit wayward, the player will end up in very heavy rough left, in another bunker right, or even worse, down a hill among trees further right.
Again, all these choices on a hole that has a remarkably easy driving challenge placed in front of the player standing on the tee.
Both these holes on a course designed more than 75 years ago. Maybe the answer lay in the fact that many of the ODG's (Old Dead Guys) simply were more creative in their ability to design long holes than most of the YLG's (Young Living Guys)...
In all seriousness, I don't think that your premise is a strong one and believe that a well-designed three-shotter that it depends on three qualities, the same three qualities it always has:
1- The quality of the site.
2- The quality of the architect to envision the holes that the site may give him to create.
3- The quality of the owner/membership in their desire to have a course designed that will bring out the best course possible that the site has to offer regardless of challenge and difficulty.