As for my personal choice, I went with a Paypal/Square combination. Overall the costs are cheaper for how I do business (primarily via phone or email) and I already had everything I needed between my computer and Android smartphone. Paypal allows me to invoice clients who use paypal and I have a Premier Advantage account that doesn't cost anything outside of transaction fees. Square is the back-up for those clients that don't like paypal and want to pay with a credit card. **TIP: if you decide to use Square, do not purchase a card reader from Radio Shack, etc. when you set up your account with Square via their website, they will send you a reader for free.
With the Paypal Premier account, I get access to invoicing, multi-order shipping (process batches instead of one at a time) and the Visa debit card that allows me to access the funds as soon as they clear. Square simply processes deposits to my personal checking account everyday that I have a transaction. So far the longest I have waited for funds to get to my bank out of the last 15 transactions was 38 hours and that was a transaction processed on a Saturday night. The main determining factor as to how long it takes is how often your bank retrieves ACH transactions from the ACH system. Larger banks do this on a daily basis whereas smaller banks may only do it every other day or so.
The main drawback to using two systems is tracking & invoicing. For Square transactions I have to generate my own invoices and then to track all my sales in the same place I need a good spreadsheet or something like Quickbooks.
When I figure that my bank (Wells Fargo) quoted me $675 in account related fees (annual, set-up, monthly and card terminal lease) and only save me approximately $2.80 per transaction, the math came out that I would have to make 241 sales this year just to break even compared to Paypal/Square.
What about website integration? Well, paypal has it's nifty little "buy me" buttons that are really easy to set-up and Square doesn't work with the web. So what happens when a client visits your site and sees paypal buttons as the only buying option? A few unofficial studies have shown that about 12% either don't like Paypal or don't know how to use it. This could mean a lost sale if they aren't in the mood to call you or it's in the wee hours of the morning when you're sleeping. An easy solution is something like Mal's E-Commerce shopping cart. The premium version is only $8/month and even if the only payment option you use it Paypal, Mal's masks the Paypal info so your client sees a normal shopping cart and enters his/her credit card like normal.
In case folks want to check things out, here are the links to the services/vendors I mentioned above:
Paypal: http://www.paypal.com
Square: http://www.squareup.com
Propay: http://propay.com
Mal's e-Commerce: http://www.mals-e.com/