There are two types of factory alarms, one that uses a remote control and the other is activated when the car is locked with the key. It is just a matter of convenience of having the keyless entry and being able to open the trunk from far away.
Factory alarms are as good quality or better than aftermarket alarms. They are very reliable and don’t usually give false alarms (unless the owner does not know how to use them, which is common). Most do lack features such as microwave, shock, glass breakage sensors, etc. and are hard to customize and upgrade.
The main problem with factory alarms is predictability. An experienced thief knows exactly what to do to disable the alarm before even breaking in the car. All factory alarms are installed the same way and in the same location for a certain model car. All they have to do is snip a single wire or remove a fuse. It only takes an experienced thief a few seconds to disable a factory security system.
Aftermarket alarms come in many different flavors, from the cheap 2-wire voltage drop sensing alarm, to high-end custom alarms that range in the $1,000s. They present more installation and configuration options, and can be easily customized and upgraded.
The predictability factor is somewhat decreased because installation depends on the installer. Different installers, even working for the same company, do different things. I said somewhat decreased because most shops use the all to common alarm wire-tied under the dash and starter disable tapped at the most accessible spot under the steering wheel column installation. This actually makes it easy for a thief because all they have to do is unplug the brain to disable the alarm. If they want to steal the car, the starter wires are already “pointed out” to them.
Even if a thief can’t get to the brain to disable it they can easily kill your alarm. Picture the following scenario: A thief breaks the glass, pops the hood, opens he hood and cuts the siren wires or battery wires. How long did the alarm made noise? Not very long, maybe a few seconds. All the people that heard the alarm probably thought, there goes another one that doesn’t how to use their alarm.
If you want a good alarm system, the best thing to do is first, tap into wires and mount the brain in inaccessible locations. The next most important thing is to install a hood lock. If they can’t open the hood, it makes it a lot harder to disable the alarm. Add a battery backup to the alarm for extra piece of mind.