Our company has processed with both third party processing and we have our own merchant account. I personally go with the third party processing even though the cost is higher but with a merchant account you need to have a person dedicated to it, managing the accounts, following up with the chargeback, monitoring the chargeback ratio and so on…
It is true that with your own merchant account you have more control on your DB and you can save on fees but down the line if you lose your merchant account you are not only losing on the processing but it will affect your company’s reputation.