Pixel himself (along with some other developers) worked on CS3D. It wasn't Nicalis who made it. By criticizing CS3D you're indirectly criticizing Pixel. If Pixel liked the end result, it means he considers it good.
There were reports around the time of CS3D's development that Pixel was directing or giving input, but in the credits in the game itself he is only listed under one vague role - "Created by." Every important role - Executive Producer, Development Director, Art Lead - are all given to other people. I'm a little skeptical with how much input he really had. It's actually not entirely clear, but given that the art style for characters and environments alike differ so drastically from every other work of art he's made, I have my doubts. The proof is in the fact the work lacks his distinct style AND if that's not enough for you, the credits also reinforce that his input was not in key development roles.
Even then, Pixel is not a god. I respect his work a lot, but he can be wrong - no one person is infallable. CS3D was not a good adaptation by any standard, even if he did give an OK to it. The staff at Nicalis is responsible for actually MAKING it. This "critiquing through proxy" standard you have is utterly ridiculous - Nicalis made the assets themselves, so they get the bulk of the critique. It's not hard.
The code for Boss Rush is the same because it is the mod. Nicalis approached this very forum for mods to include into CS+.
Getting developer consent would erase my issue with that a lot - do you have sources on the threads between Nicalis and the community? Is there any evidence that the mod creators got compensation for their work?
Did Pixel quit his day job after the wiiware release thanks to the revenue from Nicalis? Yes. Does he still get enough revenue from Nicalis? Yes.
I don't see how Nicalis is a mistake for Pixel.
Revanue-wise, it was not a mistake by any means. He's getting the compensation he deserved from the original Cave Story release. I wouldn't be surprised if Pixel views how Nicalis handles Cave Story as a more business-oriented venture than a creative one, given that he has a family to feed. And that is fine.
However, Nicalis is not the only company who could have given Pixel the ability to quit his day job. You're making the judgement from the wrong point in the timeline - it was not a mistake for Pixel to partner with a company to monetize CS. It was a mistake that he chose Nicalis. Arguably, WayForward had a similar stature to Nicalis back in the day, but their standard of custom work is much higher than Nicalis'.
I don't see how "more verbose/literary" means "more natural". When I play the game with the AGTP translation, I feel like I'm reading a book. When I play the Nicalis ports, I feel like I'm face-to-face with the characters. The AGTP translation also has/had many mistakes that are just too disappointing to even think about. (I'm looking at you, Koron, Nikumaru, and Grasstown).
This is just down to personal preference; I prefer the literary feel, personally. If you prefer the ports, that's your taste. I only have JLPT N4 (gonna take N3 in four months-ish) so I don't have the skill to discern how the translations should have been done, but yeah. Otherwise, this critique of mine is the only truly subjective one.
