It's fun to try and divine someone's intentions from an interview like this, but I guess I'd say it's not the most valuable way to approach the text. To me, the takeaway is a strong hostility to broad assertions that "Game X is better than Game Y" and a preference for more particularized evaluations.
For example, he's not saying that FO2 had a better story overall than FO:NV. He says that, "story-wise, I can definitely say Fallout 2 did a worse job on many fronts than Fallout 1, for example, and New Vegas did a lot of things even worse than Fallout 2." He gives some examples here of what he's talking about: "talking deathclaws in F2, talking animals, ghosts, Wannamingoes that look like HR Giger knock-off monsters, etc, etc.), even stuff I've done that I realized later was the wrong decision for the sake of a cheap joke (esp. 4th wall-breaking jokes)." I'm not sure what particular items in FO:NV he'd object to (I couldn't get into the game at all), but I take his point to be more that there are things in FO:NV that deserve criticism even in comparison to FO2.
It is a valuable skill in a creator (and probably in a person, period) to be able to see what is good in the things you dislike and what is bad in the things you like, so that you can emulate that good and avoid that bad, even if generally speaking you'd rather utterly condemn what you dislike and emphatically praise what you like. I think Chris has pretty consistently done this. All his talk about environmental storytelling is typically done via criticizing PS:T (a game universally lauded for its storytelling) and praising railroad shooters (which RPG players would probably generally criticize from a story standpoint).
That said, I think this particular virtue can become a vice if you don't pursue some kind of golden mean. It's an important corrective against bias and blinders, but always criticizing what you ought to love and always praising what you ought to hate can lead to a crisis of confidence, a loss of values, and a lack of action. When you're basically the one revered writer of dialogue-choice-based RPGs, to run around praising a ubiquitous form of visual storytelling can be counterproductive. When there is no limit to Bethesda's critical and financial success, and Obsidian is struggling to get by, praising the good in the former while highlighting the bad in the latter doesn't seem likely to cause the good to get better so much as to cause the good to go away and the bad to preen more.
Still, I think it's silly to take his statements as implying that he thinks poorly overall of FO:NV's storytelling or of his former colleagues.