Specs help future proof a device.
I agree with you on software 100% that's why I'm still using a 4S. The 5 doesn't DO anything my 4S can't software wise. On the same note the specs of the 4S is what is keeping it that way compared to the 4 which only real difference is less hardware speed specs.
Nowadays, any high-end phone will carry specs that will at least last you two years (long enough to get you to your next upgrade). While in theory, futureproofing sounds good, I don't think it's as much of a factor as some people would think. For example, the Snapdragon 600 and 800 aren't so different that the 600 would become obsolete, while the 800 remains relevant. They'd most likely become obsolete at the same time, even though the 800 is a little bit more powerful.
While I would agree in reference to the GS4, the GN3 seems to offer many innovative, and compelling software features in relation to the SPen. Even though most people I know don't seem to use it much.
Perhaps. Hopefully they do better with the GN3 than they did with the GS4. At some point though, it will be an situation of enough is enough, as it relates to the S-pen. Like you stated, most people don't even really use the S-Pen. Heck, I had to remind a friend of mine that she could use her's to jot down a note, when she was on a phone call looking for an ink pen lol. At some point, if they continue adding miniscule features, they run the risk of it becoming convoluted, and not any more useful that it was before. That's what I think they did with the GS4. They added a bunch of features, but in the end, it really wasn't any more useful than the GS3. Hopefully you're right, and they step it up with the GN3.