Can only speak for NIB - but the Internet banking is excellent - No OTT security requirements, ability to do instant transfers (including payments to an NIB credit card), ability to set up your own recurring payments, ability to make payments to 3rd party accounts quoting a reference number etc.
And yes, it's really free - unless you overdraw, in which case they screw you to the wall.
I've used both and I prefer the interface of NIB's online banking set-up, but there's no real difference.
I've found the branch staff to be better in PTSB, but that's only based on one branch of PTSB compared to one branch of NIB, and as you say, if you're online, hardly ever any reason to visit branches anyway.