Ecommerce credit card processing has gone a long way ever since people are finally allowed to pay online. Many merchants still do not want to dip their feet in the murky waters of possible frauds one can encounter with processing payments online. But many have also taken a plunge and saw the benefits.
If you're still doing the Paypal way, you must have encountered problems along the way. That doesn't mean Paypal is inefficient as far as ecommerce credit card processing systems go, but if you're serious about improving the way you do your business in the long term, Paypal just doesn't cut it. If you cannot apply for an affordable merchant account yet, pick a third party processor that can do better than good ol' Paypal. This takes a good deal of research as you would have to deal with compatibility issues.
Some merchants actually never used Paypal at all. The more payment methods you can use to process your customers' purchase, the better. Ecommerce credit card processing is just a small part of moving money through the Internet.