From what I've seen, the consensus is generally that the Hunter Exams are done better in '99. And some of the biggest shortcomings from an adaption standpoint are within the 2011 version, like skipping the intro episode on the island, which coincidentally includes the most significant reason Gon leaves in the first place.
And it's really not true that being a more faithful works against the argument. That's really pretty irrelevant, people just like applying significance to it when there isn't a whole lot.
Media isn't a linear construct that works simply by translating from page to motion. Fullmetal Alchemist, for example, has an excellent adaption of the early arcs in 2003. Brotherhood tends to get considered the superior version on mere virtue of being "more faithful", but the page-to-page adaption doesn't do Brotherhood any favors and in some ways makes it worse of an adaption, at least during the early sections. Basically everything up to the death of Maes is handled, honestly, somewhat poorly compared to the less faithful adaption in 2003, and even after that it took until something like the 20s to really kick off for me especially with the horribly translated comedy bits every couple minutes. That isn't a slam against FMA:B, I love the series, but it's an example of how being faithful to the manga can be a detriment to the adaption in a way the original source did not suffer from; of which I can attest FMA's manga does not have the same pacing issue, given I read quite a bit passed that point and didn't feel the same content was very uneven in manga-form.
'99 simply takes more artistic risks with the show. I appreciate that. It's still a weird show that does weird things. Like when Gon gets poisoned during the exams and spends several days paralyzed, instead of cutting to him pretty much recovered, there's half an episode dedicated to him slowly recovering and contemplating his failure. To my understanding that's not in the manga, and it's certainly not it 2011, but feels really appropriate and I don't think it would really work in a manga regardless.