Done in moderation, stroking is such an easy source of free power - as well as completely invisible in even the most meticulously original build - that I can't see any reason not to take advantage of it. The problems with it are largely from the old days - trying to use an alternate factory crank or rods that couldn't withstand high-power use. If you're going to put in new forged parts anyway, you might as well go for a 331 or 347, which has practically no downside in terms of rod angles or durability.
But to each his own. I look forward to finding an FIA build with a 260 some day.
