Java applets are dead, not much point wasting time on them, as well as pretty much all NPAPI plugin's (except probably Flash). Chrome is already planning to kill NPAPI plugins, Firefox and other are probably not going to be far behind.
You're right, NPAPI support is going to be removed from Google Chrome and Chromium:http://blog.chromium.org/2013/09/saying-goodbye-to-our-old-friend-npapi.html
Its proprietary Flash plugin already uses the Pepper API.
Plugin-less technologies are "trendy" but WebGL is still far behind JOGL (and any other actively maintained Java binding for OpenGL) as I explained in details here
and the same is true for HTML5 versus Java2D. Have you ever tried to play with Pirates love daisies
and Runestone Defense
with a Samsung S3 4G or a low end computer (AMD Sempron 2600+)? The former can't be run on the smartphone and only shows less than one frame per second on the low end computer, the latter works less badly. Breaking The Tower