Yeah, I think a five day story arc would be really good. The Disney Afternoon cartoons you mentioned only had the 4 day story arc as their first episodes which were done as two hour movies. Gargoyles had a five day story arc as their initial story that played out as half-hour episodes from Monday-Friday of its first week. And I thought that story was very well done.
Barring a week long story arc, I'd like to see them having a story thread that runs in the background for most of the season, with the last two-parter of the season wrapping that thread up.