The big thing to watch out for is hidden charges, cost of chargebacks (You'll get a few of them no matter how great your service is, mostly out of "friendly fraud"), gateway fees, etc.. These costs can rack up really fast and can turn you upside down. I'd say almost 90% of merchants out there are paying too much for their processing services.
Finally, go for a dedicated merchant account, not some 3rd party trash thats basically a reseller. With a dedicated account, you get paid almost right away into your bank, instead of weekly. Also, a 3rd party biller is many times more likely to wait until your balance gets high, then terminate your account for some make believe breach of service, possibly destroying your company in minutes. Theres very little you can do to stop this, lawsuits take forever, and even big name billers will do it to you. Be careful.