I'm glad to see there's someone else who obsesses about polls and averages the way I do.
Fascinating results, although part of the reasons why Enterprise gets such high ratings might be that 1) the notion of rating episodes online had really taken hold by then, and people who watched and liked the earlier series might not have bothered to rate them, and 2) the only people watching Enterprise by the time it got to Seasons 3 and 4 were the people who loved it anyway.
In other words, if 100 people rated TNG's "The Best of Both Worlds" and it averaged out to 8.5, but only 10 people watched the worst episode of Enterprise Season 3 but they all rated it above a 9 because they were die-hard Enterprise fans, it would seem like the Enterprise episode was better, but in fact there were more people weighing in on "Both Worlds" and therefore more chances for the number to be brought lower.
Mind you, I don't know how to fix that problem myself. I'm no mathematician. I'm just explaining what others have pointed out to me when I've done similar polls and rankings.
For instance, when I recently tallied up the viewers' ratings on the recent Doctor Who episodes on a DW forum, the much-maligned "Dinosaurs on a Spaceship" wound up in the top 5, beating such well-regarded episodes as "The Doctor's Wife." (I'm not expecting you to know what these episodes are, just that the latter was much more well-received than the former.) People who saw the rankings and knew more about math than I do were able to adjust the results so that they made more sense, but I can't figure out how they did it.
Also please keep in mind that I'm only explaining this to you to help you solve the mystery of why the results are the way they are. In no way is this a criticism of your work! You put a lot of time and effort into this, and I loved poring over the results. In fact, now I think I'm going to tally up the Doctor Who results from TV.com myself.