I would imagine in would be a parallel to comparing the 30.06 and 308, or the 280 and 7-08. Personally, I prefer more powder. I would guess that the shorter calibers are all more "inherently accurate" simply because the cases are shorter.
You can find 260 ammo, PLUS you can buy Lapua 260 brass. The only way to use Lapua brass in the 6.5-06 is to neck down 30.06 cases, and that's only my guess assuming that the 6.5 is the same body length as the 30.
In this particular situation, I'd likely go with the 260. But for the others, I prefer the long action and more powder capacity.