Have you ever looked at other credit card processors like Link point or Authorize.net?
These company`s have a lower transaction fee and a lower percentage. As a reseller for both, Linkpoint and Authorize.net
I can help you get the best deal. perhaps a Zero Set up fee.
From previous experience with Pay Pal Pro? I didn`t like it`s features...I can do the same with the regular pay pal.
About changing the Pay Pal Log on top yes you can change it.
All you have to do is host your Logo Image on a secure Server.. meaning it has to be https: or if not your customers are going to get a warning that say, something like "This web site may contain unsecured images" Click yes to proceed...
So if your customers are willing to put up with it then thats the way to go.
The Shipping feature is good but so is almost every Payment gateway out there.
Web Developer / Owner / Consultant
When starting your own business the need to "know-how" is greater than money!