You are right an rj45, rj9, rj11 , mini-xlr , mini-din all of them are better.. but none are as common, cheap and abundant as 3.5 mm jacks. They are also easy to solder and they do not require any special equipment to connect (rj11,9,45 all requires special crimping tools). This is why I went with audio jack. When I started I didnt know, later I learned and tried different things, and they work too. But I realized, this projects original goal was to keep things affordable and easy, and I found if we are little careful (which we can afford to expect, since its a DIY thing, average users will know a lot during the build phase) we can probably get away with it.
That said, anyone who is keen enough, can certainly go with better connectors, and we make it abundantly clear that this is a good idea as well. But not required.
I hope it makes sense :-) . Let me know if you all think it's not right, and I should instead go with some other connectors , cause I am actually thinking recommending the same for ato as well (i.e. connect the optical water level sensors using 4 pole TRS jacks).
On a side note, this whole connector topic is pretty fascinating in itself. I have spent weeks reading, testing and tinkering with different connectors. I would agree and accept openly that this is not a solved thing yet....at least for reef-pi.