I think sometimes "better" is just different or a change of pace from the norm. I just got back from watching my buddy in the Honda and it was brutal out there. Please don't misunderstand, PGA National is a significantly better than average golf course which, one week a year, plays as a very challenging test of the game of golf.
That doesn't make it a special golf course design at all. But many variables come into play to contribute to this.
First and obviously, it has been lengthened over recent years (how many I'm not sure) to over 7,200 yards with three holes under 375. Par is 70 rather than 72 for this event (I know, I know, par is just a number but to these guys a number is exactly what they focus on). The Honda is played during the windiest month of the year. The overseeded rye rough was pretty long, very thick at the bottom with the bermuda underneath. Several of the longer, 450+, require a layup off of the tee due to either a water hazard, fairway bunkering and/or significant pinching of the driving area.
The greens were pretty quick, fairly firm, looked very grainy and surrounded again by that considerable rough. And from a non-PGA Tour Pro perspective, a vast majority of the tee shots have either water or Oscar Bravo on one or BOTH sides of the fairway.
Please, this is just an explanation of the observations I made while watching play today in person. NONE of this makes the golf course or the event great. But, and you may include a vastly improved resort hotel here, it does set the Honda Classic apart from the run of the mill, average tour event. Six under par was the winning score. I'm willing to bet very, very few players were even par or better on the weekend. All due to the setup and conditions mostly. And all of this contributes to making a somewhat penal design (IMHO) as "difficult" and certainly different than most other events played on the tour.