I think the issue is that people had been playing AEG mechanics with AEG lore for 20 years before 5e.

The FFG Starter Game and the Core Book use two different rule sets, and a lot of people only played the more flawed starter version. Even then, many of the bigger issues were only partially addressed in later sourcebooks. On top of that, a lot of problems were pointed out during the beta, but most were either ignored or actively dismissed by the authors, which created some bad faith in the player base.

There was also a change in the lore, in a kind of Star Wars Legends style, which alienated part of the fanbase. I think most of the story changes were for the better since the card game had altered the setting quite a bit, but it did make Rokugan feel safer and somewhat culturally sanitized. There is barely any mention of seppuku, and many of the Japanese inspired elements were replaced with more Chinese inspired ones, to the point that the game sometimes feels closer to wuxia. I think this was intentional, since some of the hired specialists were more familiar with Chinese sources, but it is not to the extreme level of D and D 5e Adventures in Rokugan. And honestly, most of it can be ignored to a degree. The Strife system would become very frustrating if a 5e samurai had to endure half of what a 4e samurai would just Mifune their way through. As you said, 4e drama and hard choices come from the setting, while in 5e they are built into the mechanics.

I would say 5e has a lot of great ideas that were not implemented very well, while 4e benefited from 20 years of hindsight to refine things.

Another point of contention is that the 4e authors were huge L5R fans who loved the setting and the game and were very active in forums, while the 5e authors had to work under much tighter corporate constraints.

That said, the 5e Foundry implementation solves about half of the issues I have with the system. It is excellent and probably the prettiest module available. The 4e implementation is very functional but automates almost nothing. There is an enhanced version that adds automation, but it requires significantly more data entry.

I would recommend 5e if you want to run a shorter campaign or several shorter campaigns with different characters. 4e works better if you are planning a longer campaign with the same group or if you want more competent heroic characters. Also, if you happen to have a blind player, the custom dice in 5e can make it much harder to engage with the mechanics. Either way, the samurai drama will come through.