There are two significant differences between the 1999 and 2011 anime. The first is the story arcs covered. The 1999 anime only covers up to the Greed Island arc. Meanwhile, the 2011 anime covers up to Greed Island, then past it with the Chimera Ant and 13th Chairman arcs.  The second significant difference is in the art style. The 1999 anime has a more straightforward, grittier art style popular in the 90s and early 2000s. Meanwhile, the 2011 anime has a smoother style that is easier to animate and closer to the originating Manga style.  Besides that, both cover these arcs in mildly different ways. For example, Kite appears in the first episode of the 1999 anime to inspire Gon on his journey to becoming a Hunter. This scene is covered in the 2011 anime, but as a flashback at the beginning of the Chimera Ant Arc.