There are advantages and disadvantages to all systems - if they are one unit compartmentalized boxes or multi segmented systems. Engineering, power efficiency, and space consumption usually all rank better with one unit systems, however, if problems arise, multiple segmented systems are usually much easier to diagnose and repair than their compact system cousins.
Our company has not had experience with the Pentair or the Jandy units but we have installed quite a few Hayward (Goldline Control) systems. We have installed many Pro Logic and Aqua Plus units (both from Hayward) with little to no problems during installation, maintenance, and upkeep. Saltwater chlorination is a relatively 'new' animal in the swimming pool industry and it is slowly gaining popularity. Hayward has always been a great brand for us and continues to perform. That being said, as they are relitavely new products, there may be bugs - though I am not personally aware of any.
As with any installation, do your research - this forum is a great place to start!