I took interest in this series lately and I want to watch it. I just don't know with which one to start or with which one to continue. By the way, I have not read the manga and I know the 1999 version is unfinished and that it's a bit different from the recent version. Anyway, I just want to get the better experience.
A certain character is introduced later on in the story rather than the first episode, and the 2nd phase of the Hunter Exam is condensed. Besides that, it's accurate to the manga. The 1999 version of the Hunter Exam has lots of filler.
The 1999 version has inferior visual quality and is filled with a lot of filler. The 2011 not only looks better but it also has more story of it and remains more accurate to the Manga. So go with the latter if you want an updated and accurate depiction of the series.
I'm late to this, but the 1999 version is the best, in my opinion. I got into the series from the 2011 adaptation and like it, but find the 99 one to be superior. When they say there's "a lot more filler" that's not even really true, but remarkably, the filler is really good, except the second episode. The 2011 adaptation does change a few things around, and has some filler that even the 99 one doesn't have, like the waiting room scene where literally nothing happens, or omitting the sushi making. I also find the 11 adaptation to have some inferior visual quality, with it being digitial.