Well, to be perfectly honest, the download versions, in my experience, is more lucrative than the flash version.
As Renee mentioned, the free hour / 15 mins etc. promos on MG’s require the player to have the download software. Also, many of the new MG innovations / functions (multi language, free spins etc) require the VIPER client.
But…
I suppose it also depends on the affiliate site. If it’s a site that promotes no download casinos, and it ranks well on related terms, it would send just as many visitors, and I actually think the conversion rate (click –> registration) should be higher.