I've been looking at renders from official merchandise in which ponies are side-by side , and despite the insistnce that the Mane 6 are all the exact same body base, I've noticed that Pinkie Pie is noticeably shorter than twilight, even before Twilight became an alicorn. I've paused during episodes when at least two characters are lined up and the same distance from the foreground, and I have noticed height differences. Twilight Sparkle, Applejack, and Rarity are generally taller than Pinkie Pie and Rainbow Dash. I haven't taken a look at Fluttershy yet. It seems like there is a subtly difference. This is called Divergent Character Evolution. A similar comfirmed phenomenon is that the Cutie Mark Crusaders do look a little taller in later more recent episodes, from Season 1 to 3 and beyond. I haven't noticed one being taller than the other, but theere are subtle changes. It really looks to me that Twilie has always been taller than at least some of the others in the Mane 6.