Season six was absolutely fantastic! Totally worth the wait.
The last episode ("Red Means Stop") was great, definitely one for the ages, but it didn't really bring any resolution to this season's Blue Morpho story arc. I got the impression that it was a repeat of the situation that occurred with season five, where Jackson Publick and Doc Hammer were contractually bound to produce ten half-hours (with commercials) for the season, no more and no less, and they ended up hitting that limit before they could produce a real finale that brings the season full circle.
Last year's hourlong special ("All This and Gargantua-2") was produced as the first two episodes of season six, with production codes 601/602, but in the context of the series it really functioned as a season five finale. "Hostile Makeover" (production code 603) really was the first episode of season six, with the Venture family moving to New York.
There's still supposed to be a coming in the future. Unless Adult Swim greenlights production on a seventh season, my guess is that long-form special will come next and function as an overdue season six finale.