I am mostly satisfied with the conclusion of Innocent Venus, but I am a little disappointed that the series never seemed to reach its full potential. To be fair, it was clearly hampered by the constraints of the 12 episodes alloted to it. Given Innocent Venus' somewhat ambitious storyline; there just wasn't time to fully flesh everything out.
At least Innocent Venus had the integrity not to cave and backtrack after the episode eight twist—no flipflopping here. Like just about everything else, though, I think it would have worked even better in a longer series. Well, Gora wouldn't have been any better in a longer series, unless he was killed shortly after the "Oh shit, PIRATES!" episode.
I do wish Sana had played a more prominent role in the series (or at least a less passive one). Innocent Venus ended right when she was just starting to play a more active part.
The ending sets up the series for a possible sequel, but that's probably very unlikely to happen, barring exciting DVD sales figures. It does make me wonder if the series was based on a manga or novel, though, since I can't shake the feeling that there's more story and material out there to tell. Personally, I wouldn't mind watching a follow-up series to Innocent Venus reuniting Joe and Sana a year or two after the events of episode 12.
For some reason I can't quite understand, the final episode of Innocent Venus kept giving me Jinki:Extend vibes. The shows are only superficially alike, but the tone and style felt similar for some reason I can't quite explain. For the record, I think Innocent Venus was more successful overall than Jinki:Extend, although further comparisons between the two shows are probably unjustified.