I was the same as you at first, then the more i loaded it up the more i got to grips with it and now i love it.
To grab someone you need CQC skill equipped, then run up to the enemy and HOLD the R1 button (don't tap it), if you get it right he'll either grab em and trip em over (if you're facing em) or grab em and choke em (if you're behind em). Dont just run up to guys head on though, they'll just shoot you, try and find places where people will be unawares, such as blind drops you can stand behind or around corners works quite well too, listen for footsteps. As your CQC skill increases you get new skills, such as slitting their throats, or using them as human body shields.
The blue/red flash is the SOP, basically if you're within the flash you get linked to your teammates and can see where they are and where they're aiming - even through walls, really useful for figuring out where the enemy is. Also depending on what upgrades you or your teammates have you can share things like enemy locations via the SOP or even inject stunned opponents with hacker nanobots to hack into their SOP and see everything they see.