I previously used serial communications trough USB to exchange data with a master node. Now, i'm reconsidering this. Indeed, i'll try to give more autonomy to the arduino node, with an RTC to keep track of time. The idea being that if i want to use juste the Arduino module to control the system, i can.
I'm keeping the xml communication protocol available over USB. However, rather than plugging this node to a master node (raspberry pi), i think that i'll make it able to handle itself, as well as beeing able to recieve orders from other nodes.
Then, i'll leave the option of controlling it either from USB, with a direct connection, or trough the network, via an ESP8266.
I will thereby have a small and cheap node, capable of autonomous functionning, with the possibility to manage it via a physical interface (buttons, potentiometers, etc), or via the network, from a web browser.
I'm leaning towards this architecture because of some work i'm doing with another project, Dhomochevsky, oriented towards domotics, home automation, and smart home, and Milapli, a network of sensors for a meteo station.
Considering that the aquarium controller has many sensors, i want to be able to use those for the two other projects as well, rather than just log the data for this application. All of this will be optionnal, i'll be looking for a way to create some kind of web service to make informations available.
Anyway, now i'm working on ESP8266, and i'll probably make a new design for this aquarium controller when i get the hang of those wifi modules.