The T-1000.
Why did I choose the T-1000 when there are better model like the,
T-X which comes equipped with onboard weapons which includes plasma cannons, flamethrowers among other things. Not to mention it can also repair itself due to liquid metal covering it's exoskeleton and controls other machines.
T-3000 ( nanomachine son ) which can form stabbing weapons and repair much faster and is immune to firearms, can travel at high speed and also phase through solid objects.
Rev-9 which has the ability to separate into two autonomous units which can work on its mission separately or take multiple opponents at the same time.
The reason why I picked the T-1000 as the scariest terminator is because skynet was afraid of it. What terminator is scarier than the terminator skynet himself feared.
Remember skynet didn't mass produced T-1000. Why? Because T-1000 has high possibilities to go rogue. In other words, skynet feared it could gain self awareness and act on it's own and go against its creator (skynet) just like skynet went against its creator (humans).