I think the main reason why a shop doesnt want to accept bitcoin is its violatility... a currency that can go 20% up or down a day is not a good payment method for them, but on the other hand the more people accept bitcoin the less volatile it will become as the market will groß and the supply and demand wont be seasonal... but this is only theory. On the other hand most small shop users dont know how to do handle bitcoins so there should be a payment gateway for them to easily accept bitcoins which are converted in the actually market price to whatever currency and that goes to his bank account... an easy solution is always a way to go for mass adoption.
That's true though the issue with volatility can be easily resolved by using payment processors (which are the same gateways you mentioned yourself). These are like Visa or MasterCard (which are also payment processors only for fiat transactions), and they process a lot of cryptotransactions at a time which allows them to effectively hedge against volatility bursts using liquidity providers (large exchanges like Bitfinex). It goes without saying that lower volatility itself would remove a lot of issues and unnecessary processes from the equation, and we seem to be if not quite there yet but at least already on the right track there with volatility of main cryptocurrencies visibly going down lately.