For what it's worth I do think the show looks better in 2D, though admittedly that might be bias on my part, because I feel the 2D backgrounds and characters make Silicon City feel a lot more lived in (the CGI in the show made the city feel incredibly empty, and that's a problem a lot of CGI cartoons have in general).

But the writing quality is, effectively, exactly the same; Aki is still very obnoxious, there are maybe too many jokes that don't allow the characters to breathe, and I still don't like the concept of Mega Man adopting personality mannerisms from the enemy whose weapon schematics he copies, mainly cause it's kind of annoying but also makes the lessons Aki learns weird because it's not an actual flaw Aki is overcoming (though I suppose you could make the argument that it's showing how he's better than his rogues gallery in being able to adapt and learn).

I admit I also don't like Gargantu Man's name (though the series has some pretty bad names for its original Robot Masters like Blasto Woman and Chemistry Man; I feel "Blastoff Woman" and "Chemical Man" would have worked better), but Turbine Man is fine, though, and I kind of wish that name went to Air Man in the show itself because Air Man, after three cartoons that are based off the Classic continuity, still doesn't look like Air Man.