I don't like the fact that throughout the interview, Rodriguez speaks as if Nifflas is merely one of the designers working on the game, rather than the creator of the whole game itself. (Although he does mention "Nicklas's [game]" in passing.) It's as if the fact that Nifflas made the game is merely a selling point.
Also, at the IGF awards, each finalist was shown up on the big screen thing, with the main creator(s) of the game credited, along with whoever else has worked on the game. When Night Game came up, it went along the lines of "Night Game, by Nicalis. Tyrone Rodriguez, Nicklas Nygren, etc." That is to say, Tyrone Rodriguez was listed before Nifflas in the credits for Nifflas's game, and not for reasons of alphabetical order or anything. That really seems to me like an attempt to make those unfamiliar with Night Game to identify Night Game with the word "Nicalis" over the word "Nifflas". (Although Night Game was under development before Nicalis was incorporated.)
I'm sorry, but I just don't see it. I just reread the interview, worried that I'd missed something. I think this quote from the interview says it all:
"Anyway, It's the brainchild of Nicklas Nygren, the designer who is probably asleep from jetlag. He has an obsession with balls--those are his words, people, not mine.
Nicklas set out to make a game inspired by Marble Madness (one of his favorite games), but with his flare for ambiance."
I mean this is more than a passing mention. And I'd point out that in direct contrast to your claim that Rodriguez is implying Nifflas is just one of the designers of the game he says flat out that Nicklas is THE designer. I mean that's on top of calling the project Nifflas' brainchild and also saying that Nicklas 'set out to make a game...'. Every single sentence in this answer credits Nifflas with being the creative force behind the game. You have to twist his words an awful lot to change that.
Finally to your bit on the order of names at the IGF. I have to admit that in this case I can't just call you wrong. I do think that Nicalis wants their name associated with a game that they are likely providing a fair amount of capital and man power into. I think the thing of it is though, technically speaking they are the developer of the game and that's why their name was listed. When a game is entered in the IGF, the developer's name is associated with that game. Nifflas joined with them I would guess because they are already a registered developer with Nintendo (meaning they have a Wii development kit) and because they have the coding background to help port the game over to the Wii. Rodriguez's name came up first, because I believe he is the head of Nicalis.
And one more side note: of course they're using Nifflas' name as a selling point. A small game like this is going to need every bit of advertising and PR it can get. We Nifflas fans are probably a very small minority, but every little bit helps. And frankly I think Nifflas WANTS the game to sell well, so I can't see him complaining about his name being used to help sell HIS game.
I guess what I'm trying to say is that this isn't a conspiracy.