I have a 2013 Nexus 7 as well. And I like Sense 5 more than stock and more than TouchWiz, but I vastly prefer stock to TouchWiz. It's not a hard fact that one is better than the other (though stock Android is obviously fastest in benchmarking), just my preference.
I'd rather skin or add options via apps or custom ROMs to stock Android than rely on what Samsung decided to throw in TouchWiz by default. I won't argue if someone feels differently, it's all subjective.
I haven't used the leather-esque Note 3 myself, but it looks like an improvement over what Samsung has done in the past. It still seems like they are trying too hard to make plastic look like premium materials. It has to be some cultural thing that appeals to their Korean home market, because most of the rest of the world has since moved on from such tacky design on what are supposed to be premium phones. I guarantee you there will be few complaints if they used the same kind of soft touch plastic ASUS used for the first Nexus 7 or the current one for their phones. There can't be a huge financial hit they would take by doing so (not like they aren't making a ton of profit per phone or tablet, anyway).
It's not just the stitched leather on the Note 3 or the glossy plastic on everything else, they used fake brushed aluminum (again, plastic made to look like something else) on the ATIV S. Ultimately it's not a huge deal, but why not just use plain plastic or otherwise actual brushed aluminum?