How about two medium sized Haywards? Or Pentairs? Would the upfront be offset by the lowered run time?
I was a little concerned originally and the ledge as well but I think in the end it will be nice. It will be a 12" wide ledge 3'4" deep.
I don't know if Jandy or Pentair likes you to mess with the equipment, but once it is purchased it is yours. Be empowered, learn how it operates and do what you'd like to with it. Jandy may be just as easy, but if you were to go Pentair Easytouch or Intellitouch - I would say a requirement to add on top of that is the Screen Logic. This gives you a complete PC/Mac interface for setup of the system (and iOS and Android apps access for operation) and makes it much easier and straight forward than at the panel.
Your PB should walk you through the system you do choose and do the set up and then you can tweak it later if you like and if you like to get "into the weeds". Just knowing that you are on this site you will likely be very active with your pool and want the control, so it is up to you to learn the system. If you've got questions all of the Pentair manuals are online and there are many users here with the systems. Just reading and searching the forums for two weeks I've already learned a few things I didn't know about mine - like how to add an additional actuator even though PB told me I was maxed out and also how to use it to control a Stenner pump for Chlorine. Most everything you'd want to do - someone has probably already attempted before you and you can find the information here or ask and someone will help out.
Again - I'm not saying not to go Jandy, they may have all the capabilities you need and be able to expand as well, I have no experience with it, I'm just saying I now know what I can do with Pentair and so far really like the system and the control I have from my PC and my iOS devices.