Honestly, IF Whedon doesn't have another angle or plotline in mind that he thinks he can explore, I am fine with him moving on to a completely different webseries similar to this one. It would be fantastic to have something completely new to experience too. I do hope though that it features the talents of either NPH or Nathan in some role.
But that said, this miniuniverse Joss created has so much potential, so many character arcs, so much to offer that IF Whedon does have some ideas for it, I want him to make them into webepisodes too. 45 minutes simply seems too short a time for a universe so rich and diverse.
Including such an additional tale would make the dvd that much more appealing.
Here are my personal ideas for an angle to explore in Act 4, a way for NPH to earn his redemption.
He realizes that he feels empty without penny. So he focuses all his power and effort on cloning her or bringing her back somehow. But of course, it doesn't go according to plan. Probably if he succeeds in reviving her (he managed to freeze time afterall), she knowing who he is tells him that he can't be with him because of his "horribleness." He is upset, but seeing how unhappy she is, and esp in the anarcharist new world he created, he sets out to correct or undo his mistakes. He reshapes Captain Hammer from the crying baby into the hero that (… err… Gotham?) and Penny needs right now. Someone to believe in. He rebuilds the homeless shelter that he destroyed, bigger and better than ever. All so from the sidelines, just to make Penny happy. And penny realizing what he has done and seeign him redeem himself falls back in love with him.
That's just one possible direction. There is a lot of options. The Penny story line could be dropped altogether to focus in on a new hero, and either Dr. Horrible or some other villian from the league. And if nothing feels right, a completely different webepisode series universe would be fine.
All I ask is that Whedon not abandon the internet media potential.
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Whatever the Whedons and NPH do, I hope they don't simply return to standard media routes, especially given how long long productions can take and how quickly studios kill them off. I hope they always do such web productions on the side.