Each has their advantages and disadvantages.

A mag is less money, and might be more reliable. It depends on which electronic ignition you compare it to. A mag has weak spark at low speeds which makes it more difficult to hand start. Most people use either a spring starter (adds weight and cost) or a Miller starter (adds about $200 plus now you have to lug around that 12V truck battery and make sure to charge it). A mag is more dangerous to hand start because it has fixed ignition timing. Fixed ignition timing also makes the engine shake at low speeds. A mag has a heavy flywheel which makes the engine slow to accelerate. The heavy weight of the mag may not be a problem for tail heavy models but it is for light-tail aerobats. Lead is dirt cheap if you need to add nose weight.

The electronic ignition costs more money and you have to include a switch and a 4-cell nicad (and remember to charge it just like your receiver and transmitter). You don't need spring starters or expensive reduction starters or need to haul around the 12V battery. Hot spark at tickover speeds and variable ignition timing means easy hand starts (with safety) and low vibration. No added flywheel weight means quicker acceleration.