Most people apply for an orthopedic surgery residency (5 years?) while in their fourth year of medical school, whereas cardiothoracic surgery is a 2 year fellowship after a 5 year general surgery residency. I've heard rumors that they are thinking of changing CT surgery to something more like plastics - where you can do a couple years of general, and finish out the residency focused - but I don't know how far off in the future that is. Also, I believe you can "sneak in" to ortho by going into general surgery first. (FYI: general surgery residencies are MUCH easier to get than orthopedics)
As far as surgical specialties go, these are two of the most disparate fields out there. CT surgery is mostly intricate work (e.g., coronary artery bypass grafts, valve replacement/repair, transplants, etc.), while orthopedics is largely pretty rough (sawing off big chunks of bone, sticking huge rods into bone, etc.). Interestingly enough, the stereotypes of surgeons in these fields seem to match the type of surgery they do. CT surgeons seem to be very intense, cerebral, and oftentimes complete sociopaths. Orthopedic surgeons, on the other hand, are more of the meat-head athletes that actually discuss how much they can bench press. Of course orthopedic surgeons are not meat-heads, since it's one of the most competitive residencies out there, but I couldn't think of a better description.
That's my two cents.