I took some Pictures of both Megatrons to compare them. Here are the Pros and Cons:
Armada Megatron
PROS:
Comes with a Mini con!
Can combine with Tidal Wave
Has Electronics
Mini-con can activate various gimmicks
Cons:
It doesn't have proper knees
Poseability with the figure is limited due to the legs
Gimmicks can get in the way
"DECEPTICONS, ATTACK!" can be triggered very easily (and is very loud)
Combiner Wars Megatron
PROS:
HE HAS KNEES!
His Tank has working treads
There is a lot more articulation than the Armada figure
Dead Mini-con ports so
Lack of gimmicks give him a bit more articulation in the wrists and the legs
CONS:
Figure only slighty resembles Armada Megatron
Poseability is more harder due to the front treads being on the back (making him fall other)
No Leader-1 
Cannon on Right Arm is in the way
The 2 guns combined into 1 gun is a bit loose
YMMV:
No Gimmicks or Electronics
EDIT: OK so I forgot to mention about CW Megatron combining with Armada Tidal Wave. Apparently it is possible, but it's very loose and lacks the proper parts to do it. But since it can at least do it (remember that Tidal Wave is over 10 years old), I give the toy a +1 for being able to do that.
Last edited by Handsprime; 8th March 2015 at 10:25 PM.
I'll update this when I'm needing help finding particular figures