Honestly, even though she's not my top pick of the Mane 6, Twilight would be the character I relate to the most, being a nerd, bookworm, introverted and person who at times has trouble interacting with others initially myself. Fluttershy is also someone is also relate to, albeit less so.
To cut to the chase though, my top Mane 6 character is Applejack. Why? She has a boatload of flaws, her excessive protectiveness at times, xenophobia, stubbornness and pride for one. Yet despite them she is often willing to go outside her comfort zone to help others. Aside from that I must respect that she's a very open and sincere person, she may be blunt and harsh at times, but she's always willing to help others and be a decent person. Her and her element being orange (which makes its resemble a peach rather than an apple ironically) and my favorite being orange are just additional convenient coincidences.
As for best villain? Well Discord duh. He's basically The Joker, minus the murder and bloodlust.