Here are some tips on stealth:
Like you, early on I felt very annoyed by it. No matter what I did, enemies would easily discover me. Or so I thought.
The first trick to stealth is to make sure that your armour doesn't lower sound dampening. If I'm not wrong there's only one armour that increases sound dampening (Tactical Stealth Armour or something); everything else lowers it or doesn't touch it. It's still
fine if you lower sound dampening by -2, since that barely exceeds the threshold of the takedown range of the enemy. In other words, you still can use a takedown on the enemy if you're fast enough. Anything lower than that and the enemy will notice you before you close in on that threshold, even if you're crouching. Also, always, always crouch when you want to sneak. Running will usually alert people unless you have Shadow Running or Evasion.
Second trick to stealth is to invest in Stealth sufficiently until you get Awareness as a passive skill. Initially Awareness will need to be activated every 60 seconds (or was it 30?), so it's very annoying to manage. Once you get it as a passive skill, you can detect enemies anytime (which also leads me to my point that it makes it easier for you to notice the silly design decision of enemies spawning 2m behind you out of the blue). When you acquire that, it becomes significantly easier to sneak through a bunch of enemies.
Also, do note that crouching has a 60% chance of getting you noticed even if you think you're hiding behind cover. To ensure you have a 95% chance of not getting noticed, you'll need to hide behind cover. The problem with this is that you'll find yourself in the same predicament that I had i.e. difficult to make a run for safer grounds due to 'sticky' controls.