Whistle was a degree of sophistication, it was a degree of sophistication which they in many cases failed to actually capitalize on or provide a good enough set of recipes to use. It was used for gear leapfrogging, however, unfortunately, the actual uses of this would not really become apparent until later parts of Stormblood, which was still several years after the release, and even this was fairly nuanced in and of itself since you also had the first universal set of scrip gear in the form of Handking.
Further, I wouldn't necessarily view the overall system for crafting as complex just because it included Whistle, if you were to look at the fundamental system of crafting and arguably in general it was, for the most part lacking complexity and engagement. E.g., you weren't manually crafting because the system was complex, you were manually crafting simply because the underlying touches were Hasty Touch, and something that you wanted to eliminate as much as possible by converting excess CP (Be it via Melds or ToT) into Basic Touch or Precise Touch. The actual logic you had composing of macros were no more, nor less sophisticated than the manual crafting that 99% of people were doing.
This was entirely the problem, where there was nuance with crafting there were absolutely only a few niche use cases for it, and unless it's something that could be much more widely adopted was just a wasted system. It was also a horrifically unbalanced system wherein if you learned even the fundamentals - You could pull very inane stunts such as the one below, this is something that never, ever should have been doable, as fun as it was. Contrary to my post in that thread, I do think Whistle would have been more harm than good if introduced with current experts - It's a system that downright needed redesigning more than anything.
Job complexity aside or lack thereof, the player base is largely just better now than it was. To put it into perspective, do you think people would be wiping in droves like they once were had Weeping City and Dun Scaith been introduced now instead of in HW? The only wipes I've experienced have been from some unfortunate sprout getting the meteor markers in Ozma and thus wiping their party. otherwise it goes down just as all the others do.
I'm going to half-agree with you here in that there is a place for exploratory content, but it is a place that should exist natively in the general overworld zones. e.g., Ahm Araeng, Tempest. The fact that players would need to do this content and that it is not experienced naturally in the standard zones is a big problem. It shouldn't exist as side-content it should be naturally embedded in every single zone in the game.
Edit: That I got that tangent off my mind; I think the copy and pasting job has been in varying amounts and to a varying degree. For the most part with many games, you'll inevitably find yourself going down this route. e.g., SE didn't think people liked deep dungeon, so didn't inc. in ShB - People complained, so they reintroduced it. The same would apply to exploratory content sooner than later when they've exhausted their creativity with it. E.g., Logos were just copied and pasted into Essences. BA was just copied and pasted from EM in that function, I would like to say (to some degree), just as CLL and Zadnor were copied and pasted features from BA.
Further replies I'll likely attach to this post or subsequent ones provided the discussion is worthwhile (Probably nearing cap on my post-count for the day)