Disc swapping should never be deal breaking, and only idiots let it be.
It's a valid reason to go for one version or the other, but the closest I can see to it being legitimately deal breaking is if, say, Baldur's Gates disc swaps really annoyed you, so you'd rather wait on other Infinity Engine games until you upgrade your harddrive and can fully install the games easily. Not that that's an issue for modern PC gaming, but it's a point I'd find legitimate, especially since disc swapping functioned differently from the console RPGs most of us were likely more familiar with at the time.