If you are confused about which system to get (Ardupilot Mega 2.5 or 2.6) this will hopefully help you out! I will outline some of the differences between the two aprat from the little number on the board. I will keep this brief so you can quickly decide but if there are any questions please ask!
Both APM2.5 and 2.6 have exactly the same hardware and sensors, the only difference between the two is that in APM2.6, the compass sensor is taken off and is now included with the Ublox GPS/Compass module.
- APM2.5 reqires the Mediatek GPS module as the compass is built in
- APM2.6 requires the Ublox GPS/Compass module
Both the APM2.5 and APM2.6 boards run the same software, there is no difference.
Because the APM2.6 uses a different GPS module and has the compass externally it is slightly more expensive than the APM2.5.
Which one should I get?
This will mainly depend on what platform you are flying.
Fixed Wing - if you are flying a plane then I would suggest you go with the APM2.5 as its slightly cheaper and due to the space you can mount the APM away from magnetic interference (motors/ESC). Also the higher speed Mediatek module it better suited to faster moving vehicles.
Multi Rotor - if you are flying a quadcopter/hexa etc.. then its best to go with the APM2.6 as the GPS module is better suited to slower moving platforms, and the external compass allows you to mount it away from interferance from all the ESC's you have on Multicopters!
However there is still no problem with using APM2.5 on multirotors, and APM2.6 on fixed wing, this is just a guide