I'm still catching up, I'm currently halfway through Season 9. But I would rank seasons 1-8 this way (although I might change my mind later).
A few caveats: I watched all these on Netflix or DVD, so season breaks and airing times didn’t affect my enjoyment like they might have for these who watched them as they aired. I’ve also rewatched more of the Davies era than the Moffat era, so that might be affecting things; I might find this list later on and find I’ve changed my mind. And yes, I know that it’s not really fair to pit the “specials years” against the rest of them, but it won’t really hurt anything, will it?
(“Favs” means episodes that I would label as “favorites”. I have a lot of those, ha ha. More favorites than non-favorites, in fact. I know that sounds improbable, but what can I say, I love Doctor Who. I’m counting Christmas specials as part of whatever season Wikipedia sorts them into. And "Dalek Eps" is a combination of how many Dalek episodes are in a season and how much I enjoy them. I have a special love for Dalek episodes, lol.)
Season 1:
• 10 Favs
• Dalek Eps: 8
• Finale: 8
• Doctor: 4
• Companions: 8
• Arc Villain: 5
• Score: 43
Season 2:
• 9 Favs
• Dalek Eps: 6
• Finale: 10
• Doctor: 3
• Companions: 10
• Arc Villain: 8
• Score: 46
Season 3:
• 8 Favs
• Dalek Eps: 3
• Finale: 3
• Doctor: 3
• Companions: 3
• Arc Villain: 6
• Score: 26
Season 4:
• 9 Favs
• Dalek Eps: 7
• Finale: 7
• Doctor: 3
• Companions: 5
• Arc Villain: 4
• Score: 35
\
2008-2010 Specials:
• 4 Favs
• Finale: 5
• Doctor: 3
• Companions: 2
• Arc Villain: 10
• Score: 24
Season 5:
• 10 Favs
• Doctor: 1
• Dalek Eps: 2
• Finale: 9
• Companions: 9
• Arc Villain: 7
• Score: 38
Season 6:
• 12 Favs
• Doctor: 1
• Finale: 1
• Companions: 7
• Arc Villain: 3
• Score: 24
Season 7:
• 11 Favs
• Doctor: 1
• Dalek Eps: 5
• Finale: 2
• Companions: 4
• Arc Villain: 2
• Score: 25
2013 Specials:
• 2 Favs
• Doctor: 1
• Dalek Eps: 4
• Companions: 1
• Finale: 4
• Arc Villain: 1
• Score: 13
Season 8:
• 10 Favs
• Dalek Eps: 1
• Doctor: 2
• Finale: 6
• Companions: 6
• Arc Villain: 9
• Score: 34
THE FINAL SCORING:
2013 Specials: 13
2008-2010 Specials: 24
Season 6: 24
Season 7: 25
Season 3: 26
Season 8: 34
Season 4: 35
Season 5: 38
Season 1: 43
Season 2: 46
So there we have it. There are some really interesting tidbits here, like how Season 6, despite having the most episodes that I individually liked, had the lowest score aside from the specials years. But the numbers don’t lie!
Is this a perfect scoring system? No. But I feel that the results accurately represent my feelings, and that’s what really counts.