As everyone pointed out, the fact that a compny is using a 3rd party processer doesn't mean they provide poor quality service. Out of many things, it can also mean the company would like to cut its costs and possibly even invest it support services, areas where it can see more value for every dollar invested.
I would, however, prefer not to deal with companies that accept PayPal as their only payment solution. Getting a paypal account is easier than a real merchant one, and legal business age is one of those problems. When I see a company that accepts CC, I have at least some confidence the owner was passed through a more serious screening.
Best,