It is definitely the best-written of all the currently-running Marvel cartoons.
I think the clear difference is that one instance has Black Panther in a team context (EMH, Avengers Assemble), while the other has him in a solo context with the team tacked on (Panther's Quest), so the dynamic and handling of T'Challa is going to be demonstrably different because the latter is obviously going to better serve and cater to that one individual character since it's their solo cartoon.
I did like EMH Panther's costume with the purple accents and the way they handled the daggers was really cool and unique visually.
I definitely think the weakest part of Black Panther's Quest is the animation. In general it just looks more generic and cheap then it should be, only looking marginally more better then Marvel's Spider-Man, which isn't saying much (just hop on over to that show's thread to see all the complaints about the animation).
And a lot of the character redesigns just haven't won me over to be honest, outside T'Challa and Shuri. Actually, I think the Black Panther characters are the ones who generally look the best, design-wise, compared to the Avengers characters.