If I understand your post correctly, you don't want to see (for example) "Big Bang Theory, Season 1", "Big Bang Theory, Season 2", etc etc when you view your TV episodes on AppleTV, is that right? You just want to see "Big Bang Theory"? It's an annoyance I face too, given I have so many TV shows with multiple seasons in each. It's frustrating that iTunes/AppleTV interface doesn't implement the same folder structure that is given to the actual files on my Mac, where each season of a TV show is grouped together inside of a folder that is just the show name.
There isn't really any good solution, however you can, if you like, have all the episodes of a show grouped together, with the trade-off being that they will no longer be in separate seasons. To do this you would remove the season number from all of the episodes, and instead keep the chronology of episodes by changing the Disc Number to be the old season number. So to use the screengrabs in the post above to explain what I mean, you would remove the "6" from the "Season Number" field, and change the fields under "Disc Number" to be "6 of 6". If the episode was from Season 5, you would have changed the "Disc Number" field to read "5 of 6".
I'm not a fan of this approach since, when I have shows with 8 or 9 or more seasons and 22-24 episodes a season it becomes too hard to locate a particular episode, but as far as I know, that's the only solution that lets you retain episode numbers, while removing each season appearing as a separate item within the iTunes/AppleTV interface. Basically you trade off your initial list of shows being too long and complicated to navigate with your list of episodes being too long and complicated to navigate.
EDIT: I just rechecked this method using my converted episodes of Seinfeld, and frustratingly it wanted to sort all episode 1's, then 2's and so on. I'm sure I have seen it keep them in chronological order somehow, you might want to try editing both the episode number and/or the episode ID to reflect the following notation - Season-numberEpisode-number, so, for example, the 5th episode of season 1 would be 105, the 12th episode of season 8 would be 812, etc.