Don't worry, 'some people' are very sad and can never consider there might be a 'bigger picture'. ;-(
It probably is ... but how about, replacing the panel connectors with something from the Anderson connector range (polarised, self cleaning, non-locking) and bring them into the controller on a bundle of 5 wires, terminating as one (pair). That way you can mix-n-match panel combinations easily and if someone moves a panel away or trips over the cable, no harm would be done.
The layout of the batteries may come down to what you can handle physically. I have 3 x 34Ah semi traction batteries that I intend to use in parallel with an electric outboard (chosen as being the heaviest the Mrs could take off me individually and lower into a boat) and then to sit in a custom wooden tray / box that is fitted around the shape of the hull.
Again, if the battery combinations were on Anderson connectors, it would make it more flexible.
A small batch of 'Smart' (12V would be the cheapest) chargers to either leave on or move between the battery pairs in series would both safely keep them charged and prep them for use when it's an overcast day.
Keep the high current cable runs (controller <> batteries) as short and as heavy conductor as possible. A fuse on / as the battery pair interlink might be a good idea (in case one battery goes short and the other try to charge it).
Even if sealed batteries, keep them well ventilated.
Have fun. ;-)
Cheers, T i m