Yes a flat twin is obviously a little better than a single piston thumper. Vibration is the reason electric has taken over in the small arena.Along with simplicity as well. Vibration can be solved, perhaps you should ask the guys at the http://www.uavfactory.com
All the fixes have been mentioned.
Engine mounts,isolation,balance props,mount IMU in a vibration free floating manner
Anyone developing for North America should think that time as well as speed limits will apply when the regs change so developing flight times of greater than 30 minutes for non COA airframes may become a little pointless.
The new version of the FY3ZT autopilot comes with a new Vibration damper and Alu case. This improved the vibration issue from Gas engines alot.
Some inspiration pictures
this solution doesn't dump all vibration (only small vibration), for small vibration i use magic gel
Any single cylinder engine has this problem, one of the best solutions is to find some isolastic (rubber) mounts.
when balancing a single cylinder engine you don't really "balance" them, rather the vibration is distributed evenly vertically and horizontally.
First check the prop and see if it is way out of balance,drilled off center or cracked.
Also, when running your engine do you have the wing(s) installed? I have a Great planes Giant Big Stik with a 40cc and the fuselage will vibrate like crazy without the wings.
Magnetic mounting plate will do the trick. There are mag plates above and below the magnetic plate that stays centered when either if the other magnetic plates move.Mount electronics to the center plate.
Similar technology as the magnetic levitation trains.
One big drawback is the magnetometer goes crazy, but the other sensors are vibration free.
Also check your ignition timing as this can be a source of extra vibration and poor running.