1) His gender and general nature. He's not the typical Fluttershy healer who is all nice and friendly. Snakebite's a male healer and not the nicest pony found, but he'll help. I also like that he is more in tune with the way the Wasteland works than other healers.
2) He isn't defined solely by being an alicorn. He has his history with his teacher, giving him insight to zebra culture and customs. He likes energy weapons over regular guns. He is mature, and not easily riled up. Those little things help making him much more than yet another alicorn reawakened.
Also, I like the much more smaller scale style of the story, and focus much more on the towns that were created after the megaspells hit. That combined with Snakrbite's own history of growing up in the wasteland, offer a different and less negative view on the setting than say from Littlepip.
Start the Power of Atom quest. Before disarming the bomb, go into Moriarty's Tavern and talk to the man in the suit sitting to the right of the door. He'll ask you to arm the bomb to explode. Once you're through talking to him, go tell Simms about him. Simms will then go to arrest the man and the man will proceed to kill Simms. Kill the guy, loot the bodies, disarm the bomb, and talk to Simms' son. Along with the regular rewards for completing the quest, you'll get Simms' hat and duster along with a Chinese assault rifle and a silenced 10mm pistol and there will be no Karma loss. No one will turn hostile on you for shooting the man either.
Alternatively, get the law bringer perk, go to the Regulator's HQ, and talk to the lady in charge, she'll give you a Regulator Duster which is more or less identical to the one you get off of Simms.
It's so... obvious. After talking to Moriarty once and buying out his stock, I never wander over to that side of Megaton again. I guess I could have looked it up, but... Well, I guess I'll have to try this now.