Hi freetodream,
I haven't run the numbers on it, and I don't run a shop yet, just so you know. However, from my research on everything so far, I would venture that the flavored beans are going to be more cost-effective on a straight up basis. However, if you don't have a big enough demand for flavored then you would probably need to factor in the cost of the extra grinder plus the extra carafes/airpots etc. From what I've read about it some flavored coffees are so strong you have to dedicate a carafe to them. Then factor in wasted coffee if you're not selling each pot in a reasonable amount of time....and the issue gets murkier...know what I mean?
Again, it's all going to come down to your customer base and whether or not there will be enough demand. I know that some shops can't seem to stock enough flavors.....others none at all.
I'm thinking mine will have very little demand for flavoreds....I hope :-D