I don’t have much of a preference. I have read both and enjoyed it. They can even switch for more fun :D
Hmm, the Doctor has used many alias during the time of the show (you can look them up here). The fan favourite seems to be John Smith so if you want to be on the safe side, you can use that one.
I would suggest to use the actor name if you don’t want to go with John Smith. I know I would find it very hard to follow a whole story where the Doctor is called Oliver or Maximilian because I don’t associate these name with him, whereas I will easily be able to picture your character as the Doctor if he is called Matt, David or Christopher.
Obviously those are my personal opinion and I’m sure our followers could help here?
EDIT: I guess you are talking about this made with Philip Bond: http://www.bleedingcool.com/2012/08/17/philip-bond-to-draw-doctor-who-comic/
First issue in a special two-part story featuring the art of Philip Bond! The stress from their past few adventures have the Doctor and Rory at each other’s throats, and Amy has had just about enough. So she sends them on a boys night out, must to their chagrin, but with a TARDIS at their disposal…
Seems like he will work with Brand Seifert on it. http://www.idwpublishing.com/news/article/2401/
I love it, it’s so true for them! It show how much they can be alike, and how Rory came to like the traveling and held the Doctor close to his heart, even when Amy was the center of his world.

From The Power of Three :)
Oh.My.God.
http://www.youtube.com/watch?v=qyjraokQy9E
Anybody feeling like doing a video to this song? Because this is perfection in a song.

Thank you, I’m sure you will come to hate us for that.
I hadn’t seen it that way but it’s true ^-^. I bet that even back in the old day, Rory still had fun dressing up as the Raggedy man!
Ah. You got me there I don’t follow/know any really. I quite enjoy Gatiss tag http://gatiss.tumblr.com/tagged/brotp for them.
The ship is too small to have ever made people dedicate blog to them. At least, that I know of.
So I’m going to ask my followers. Your favourite Eleven/Rory blogs?

We don’t want them to go. Because the Pond need their Doctor and the Doctor need his silly little Pond. No more fish fingers and custard on the couch.
We don’t want their fairy tale to end :(

He was, I didn’t notice…
Chibnall is the Patron saint of our ship. All hail to his scripts!
YES CAN WE? BECAUSE IF THIS ISN’T THE LOOK OF SOME PROUD SPACE HUSBAND, I DON’T KNOW WHAT IT IS.

Hello there!

Welcome to the beauty that is the Doctor Who fandom and it’s nice somewhat mad fans.
You are asking a loaded question but I will try to answer seriously. The relationship between Rory and the Doctor is complicated because it goes very far back into Rory’s life, but since you haven’t watched yet, I don’t want to give too much away.
The relationship between Rory and the Doctor is not a love one from the beginning. Rory is insecure and jealous of the Doctor who, from his perspective, took his fiancé away. He isn’t very impressed by the Doctor and his Tardis, showing off his nerdy side, which seems to both annoy and delight the Doctor.

From there, their relationship evolve to the point where the Doctor confess to Amy that he rather likes Rory.

This is a deleted scene, but I still think of it as the one that got many people realizing that the Doctor might just have a little crush on Rory. And considering how this episode ends, we know Rory did come to like the Doctor too.
It only gets better from there, with sexy centurion and phallic metaphors

I won’t lie and say this pairing got a lot of scenes or is very canon. It’s not, mostly because seasons 5-6 were a lot about Amy/Rory and Amy/Doctor relationship, leaving a big hole when it comes to the Doctor and Rory. Doesn’t mean we don’t like to fill it or that the writers forget about us

Or the cast

But it’s not the biggest slash pairing you will find in Doctor Who, or the most popular one. It’s still a cozy and happy one.