flthis is mine
1 fluttershy
2 twilight
3 rainbow dash
4 rarity
5 pinkey pie
6 apple jack

I probably disagree the most with Fluttershy, but meh. We all have opinions, and when on the internet, opinions are of course 'strictly forbidden.'
Twilight deserves better than being called OP or a Mary Sue. She is my 4th favorite Mane 6, but it's just because I think Fluttershy, Pinkie Pie and Rainbow Dash are slightly better than her.

Only one we have in common....sorry.

List:

1.Fluttershy
2.Rainbow Dash
3.Twilight Sparkle
4.Rarity
5.Applejack
6.Pinkie Pie

^You putted Twi and Rainbow at the same spot didn't you?

Here's mine
1 and 2.Pinkie pie or Twilight
3.Rarity
4.Applejack
5.Rainbow dash
6.Fluttershy

Here's my list:

1. Rainbow Dash
2. Rarity
3. Pinkie Pie
4. Fluttershy
5. Applejack
6. Twilight Sparkle

^ Why Twi last?

None of the them are in my order, but Applejack is the closest:

1. Fluttershy
2. Pinkie Pie
3. Rarity
4. Rainbow Dash and Twilight Sparkle (tied)
5. Rainbow Dash and Twilight Sparkle (tied)
6. Applejack

That's a tough one, because my own order is completely different to this. I think mine order currently is:

1. Fluttershy
2. Applejack
3. Rarity
4. Rainbow Dash
5. Twilight Sparkle
6. Pinkie Pie

My order changes a lot though! So going by that, my top two are your bottom two, and all the others are two spaces different. Went with Rarity though because, although she is not my absolute favourite, I love the top three on my list a fair amount more than the next three. So basically I love her and I'm glad to see that even though she's not the top of my list, she is the top of yours!

That said, I adore all six of them really!