Well it's because of they (Skyrim and New Vegas) show what potential the other one had and didn't fulfill.
There was no reason Skyrim couldn't have as much dialog and story as New Vegas, and yet it barely has any. Likewise, New Vegas didn't do much for scenery, some might argue, though wtf it IS a desert. Not to mention the other day I went to Zion in Honest Hearts and thought "wait a minute, this entire map was built from the ground up by Obsidian, and it can look just as nice and realistic as some of the mountains of Skyrim." More dated graphics of course, but the detail of the area is on par with that of Skyrim.
Basically, we compare them because we're frustrated Skyrim was such a let-down and the comparisons provide logical reasons for why Skyrim could've/should've been better.
Partially i agree with all that you said, and im playing both series since their very first games (tes:arena and fallout 1), and i can say that fallout 1&2 are my favourite games of all time, so dont think im dovakhin or something. I just meant its not fair to say "fallout has this, skyrim doesnt, fail skyrim". The developers of skyrim had other goals in the game design, and i doubt it was possible to write each and every npc so detailed and dramatic as they are in new vegas. New vegas is about following the story, making choices, fighting, while skyrim (as any other tes game has always been) is more like a simulation of a huge world which doesnt really care about protagonist and doesnt need you to do any quests. And actually skyrim made a huge step in detail compared to morrowind for example. What really let skyrim down is that its so much console-oriented (new vegas too btw, but its almost unnoticeable). Sloppy unresponsive interface, simplification of everything and a ton of glitches, at least on the PC version. I wont bother writing my pc specs, but im playing battlefield 3 on 64 player maps every setting ultra and fps never drops below 80. And skyrim somehow manages to drop to 10-15 all the time, and i still havent found the solution, so thats why i quit skyrim. Sad, thats a great game, too bad i cant play it.
tl;dr: skyrim's storyline is pathetic, but no need to compare it to new vegas, both great games and both different.