In theory the bigger bore size burning similar powder charges will lose less speed so the 6.5 should lose a LITTLE less speed in a shorter barrel. But it ain't enough to worry about. I've compared 308 and 3006 with barrels ranging from 18"-24". Chopping 4" from a 3006 will cost you around 100 fps. Chop the same 4" from a 308 and you lose about 75-80 fps. Yea, the 308 is more efficient, but the 3006 starts 100-150 fps faster. It is still faster with the 4" shorter barrel.
I'd shoot hogs, deer or Coyote with a 223 out to 200ish, Coyote much farther. If you're shooting hogs or deer at 400+ I'd go bigger, and I really like the 6.5 best of those 3. The 243 just isn't enough jump over 223. I'd not let barrel length effect my decision.
