What Could Have Been:

Pretty Cure is not #1 because it's some sort of unstoppable juggernaut of quality.  It has plenty of flaws and weaknesses.  It's just that no one else is being given the level of support Pretty Cure has received.  If other stories were animated in full like Pretty Cure is, any number of contenders could possibly surpass the current #1.  In a more ideal world, these guys could all be ranked higher than Pretty Cure.  Potential #1's if a franchise were finished being made and then fully and perfectly adapted:

Clannad
Sword Art Online
Bake-(etc)-monogatari
Fate/Etc
Fairy Tail
Mahou Shoujo Lyrical Nanoha
Little Busters!
Higurashi/Umineko no Naku Koro Ni
Seikai no Monshou/Senki/Danshou
To Aru Majutsu no Index/Kagaku no Railgun
Full Metal Panic!
Ranma 1/2
Major
Da Capo
Papa no Iukoto wo Kikinasai
Hayate no Gotoku
Saki
Maria-sama ga Miteru
World of Witches
Boku ha Tomodachi ga Sukunai
Haruhi Suzumiya
The World God Only Knows
Rurouni Kenshin
Utawarerumono
Shirobako
Berserk
Maji de Watashi ni Koi Shinasai!
Hai to Gensou no Grimgar
Sailor Moon
Tales of 'x'
Eromanga Sensei
Suka Suka
Youjo Senki
Outbreak Company
Claymore
Akame ga Kill!
Akatsuki no Yona
Gate
Rewrite
Btooom!
Juuou Mujin no Fafnir
Negima/UQ Holder
Freezing
Kono Oozora ni, Tsubasa wo Hirogete
12 Kingdoms

I'm not saying these shows would definitely beat Pretty Cure, I would have to actually see to judge.  But I think they're close enough in the ballpark that there's a chance such a thing could happen with any of these 45 franchises.

This is what makes my rankings so frustrating.  The place a show ends up in my rankings says nothing about their innate quality as a source material, and their potential if only they were adapted faithfully.

Freezing could be the best story ever and it doesn't even appear in my anime rankings!

This is also why my anime wishlist is so important.  If you consider a #1 show being worth at least 10 average ranked series, if we produced in effect 45 additional #1's, that would be like creating 450 new great anime series, or in other words, tripling the quality of anime overnight.  Add in the other 55 wishes on my wishlist and we could be talking about quintupling the quality of anime.  Anime has so much more potential than what it's shown the world so far.  With a proper charitable billionaire, we could produce all these shows and more even at a loss, and the world would be so indescribably more beautiful for it.  Anime is already the best thing on earth, so can you even imagine how joyous it would be if it were five times better?