So... now when selling anything online you need a separate price tag for every country people might be buying from? That is assuming you want the same return from every buyer.
Don't take my following words as authority as I don't have my business license yet...
To get the same return from every buyer, your price should be tagged without VAT and so, it pretty much depends through which service you sell your game.
I'll take "Loren The Amazon Princess" from Winter Wolves as example:
Through BMT Micro, the base price is 19,99€ and the local VAT is added during the purchase process so as a Belgian customer, I'll pay 24,19€. 4,20€ goes to the VAT and 19,99€ goes to the dev (without calculating transaction fees of course). So, with this system, you're sure to always get the same return per purchase.
Through Steam, every price is VAT included. Loren is shown at 19,99€ on steam page. So, you substract 21% (Belgian VAT rate), it leaves you with 16,52€. As in 2015, EU VAT will vary, you'll always have varying rates and incomes from different EU customers, you'll need to double your spreadsheets (one for the different VAT's to pay and one for the different net incomes). By the way, don't forget the 30% steam share cut...
As you see, it's much easier to keep track of accountability if you choose the "VAT not included" model. Maybe steam has the option to do this but I've never seen it as a customer.
TeeGee sells Cinders both through BMT Micro and Steam so maybe you could ask him how he foresees this situation.
EDIT: Well, you can also put different price tags for every EU country with locat VAT rate included if you want to keep your net income constant per customer but I think it will get confusing.