"Does it really make a difference to you which Fallout is treated as the better one?"
Yes. Why? Because, contrary to popular opinion, developers want to know how their audience feels about what they've made.
We have something special here, two semi-sequels to an old-but-great game series done by different studios in different ways, AND a new game coming up. Both were good games in and of themselves, but if anything could have been done better in either of them, the devs need to know so they can use that in the next one. And hopefully make the sequel the best fallout yet.
Personally, I think New Vegas was much more in line with the games before it story-wise, using the factions from 1 and 2 in a relatively logical manner. 3 was a very good game, but the plot simply made no sense. Why were those factions there? I'm pretty sure (obscurified spoiler) I destroyed one of em in fo2. And the others behaved nothing like the rest of their kind did in previous games. On the other hand, New Vegas was rather empty (the city, not the game) and it was quite the buggy mess on release.
If these discussions lead to the devs picking the discussion-flaunted good points from both games and fixing the not-so-good parts about them, then that is a good thing.