What are you wanting to achieve?
You can shoot any format of film and finish to HD 1080p and it will look fine, obviously the better formats like 35mm, super35, 70mm and variants will all look good and typically superior than super16mm, but a good super16 cam in a pro's hands could look terrific in HD. So the medium you use all depends on your budget and desired look.
As for markings, 16x9 is fine for HDTV but what about legacy standard definition? Are they going to letterbox it? Are they going to pan and scan it (its still standard practice)? Are you sure you don't want to frame it for 4x3? Really, without you telling us what you want to produce and where its going, there's no way to tell you any exact answers.