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!
Hardware
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
Software
Both the APM2.5 and APM2.6 boards run the same software, there is no difference.
Price
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.
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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.
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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 
can you give me suggestion about where I can put the GPS with compass on APM 2.6 to reduce the inference? I mean I can’t see anywhere without the base plate. So what would be the difference between apm 2.5 and 2.6? because in 2.5 the compass in on the board which is also on the base plate.
APM 2.0 had an onboard GPS and compass as shown below
Then APM 2.5 was released which had an external GPS to allow for more flexibility as to where you can mount the APM and GPS for best signal.
Then APM 2.6 was released which now has an external GPS and compass, as for multirotors in specific, the compass plays quite a big role in good position hold (when you are not moving you only use compass for heading)
As for GPS (or for GPS with compass) its best to mount it with a clear view of the sky (not under carbon fiber plates) But if your frame uses plastic parts, or foam, its ok to mount it under this. But most important is to keep it away from your motors/ESC. And if using telemetry, also mount it at least a couple cm away from that.
You can also use a GPS mount which makes it easy to mount your GPS/Compass away from interference.
Can I use APM2.6 without using external GPS/compass module?
Hi
Yes you can use the APM2.6 but then it will just be a flight stabilisation device and you cant use it for things like position hold, or waypoint flight as these flight modes require the GPS and compass. 
What does flight stabilisation mean exactly? I have a remote control can I control it using it?
It just means that it will keep your aircraft level, so if you let go of the sticks it will go back to the level flying position. With the onboard pressure sensor you will also be able to maintain altitude too. But for hover flight, loiter, or waypoint flight you will need to use a GPS/Compass module.
Hope that explains it
