Sure, If you go 243 you will get:
Short Action= less weight+faster bolt manipulation
WAY better bullet selection
WAY better Ballistic coefficient options
With the 25-06 you will get:
Heavier bullets with a poor BC
(115 VLD will net you all of .466)
A little more poop on the receiving end (moderate range).
A higher cross sectional area
Might net more velocity
If you are limiting the game size up to Deer & 'lopes only, I have got to vote 243, flat out, hands down winner IMHO. If you intend to throw heavier critters in to the mix (elk) I would probably vote 25-06 for more bullet weight (a whopping 5grains) & diameter.
The 6mm bore size is getting a LOT more attention than the quarterbore, which means better component selection.