The 2.39:1 actaully looked pretty good except for the opening shot, which could be fixed by re-framing it, when you do a wider aspect ratio like 2.39:1 you have the option of moving the image up and down vertically and sometime taking the same amount off the top and bottom is not the best framing option, here's how I would frame the opening shot:

Keep the sort of shots you plan to use in the film in mind, when I used a 2:1 aspect ratio in Manhole, I did it because I knew I would have shots like this which really benefited from a wider aspect ratio, however in my current film there is a lot of talking and even some vertical movement which makes me want a taller aspect ratio, so I will be shooting in 16:9. If you have a lot of expansive wide sets and shots, wider will work a lot better, however if you have more height or vertical movement in your film you might want a taller ratio like 16:9. Personally I think it's silly to shoot a film in a really wide ratio without really working to make sure your sets have a lot of horizontal depth.

Thanks for the advice guys! I think since the main bit of the video will be him in an arena then a wider aspect ratio will probably be ideal as I don't want to be able to see much of what is above him, I'd quite like it to have a claustrophobic feeling. I adjusted the framing of a few shots based on what SlothPaladin had done and I think they look better: https://www.youtube.com/watch?v=bQIkFtQ5YmY

I'm not an expert on aspect ratios.
I am just here to comment on the fact that the animation was outstanding. It felt like I was watching the magic portal (probably because of the face print). It somehow feels a lot better to watch those faces as to official lego heads. Whatever you did, I am looking forward to it (that is if it's a complete film and not a test). Even if it was five seconds, I am very interested of what's happening.