Lyman - on my RaceMeasure site, I have an Excel spreadsheet that allows you to put in your Jones start count, and it will tell you where your splits are. There is a free app that will allow you to edit spreadsheets. Kingsoft Office. Disadvantage of this free app is, I don't believe you can edit multiple sheets in one doc. I wasn't able to, and have gone back to using my paid (Documents To go) application. But, put your Jones count in, and all splits calculate, based on your calibration rides entered in the sheet.
I have no issues with judging my .02, or .03 revolution, as each .05 revolution is very close to one Jones click. So, if I am off .01 revolution, I still have more accuracy that a Jones rounded to the nearest click.
The biggest disadvantage I would see with a Protoge is when you overshoot a mark. You cannot reverse the counts in a Protoge. I use an electronic Totalizer from Veeder-Root. It has to be wired, and I had to get a magnet and wire from a cheap cyclometer, along with a couple of small switches, but I can ride my bike with my counter counting down, if I overshoot. Or, I can roll it backwards, after flipping the switch, and it will count down.
The electronic method is not for the faint of heart. It takes time to set up, and you have to get parts from Radio Shack. Also, you cannot stop with the magnet next to the sensor, or you will get spurious counts. That is the most important aspect to be aware of - never stop at "zero" on your wheel.
The JO has "slop" due to gearing inside. There is no way to (relatively) cheaply produce the counter so it has no slack. I also round to the half-click, but if you are not rolling forward to the mark, there will be slack that can impact your counts by a full click. Not the end of the world, but in calibration rides it makes a difference.