Yeah, cool idea but bad in a real world situation. I reckon it'd be too unreliable. Also not all phones would support it or vice-versa. What happens if your phone goes flat and you don't have a charger? Or drown the phone while out fishing, or in torrential rain or drop it in the loo or something?
I say stick to the wireless key, they're relatively waterproof, reliable and have a back up old fashioned key for if they die.
As for security, if these mobile phone systems were common thieves would just start stealing both the keys and the owner's phone. Most factory immobilisers are that good now that you need the key to start the car, so thieves are breaking into houses and stealing keys along with the car, or when people leave them unattended in public.