EatChildren
Currently polling second in Australia's federal election (first in the Gold Coast), this feral may one day be your Bogan King.
Shiieeeet...
EatChildren, cant you record a sensual, intimate clip for me to fall asleep to? Dat voice.
Said nobody ever about a bogan accent

So a game mechanic that's very risk/reward is now considered a problem?
It's now a problem because the necessity to use additional tools has been diminished. You've got the tools but you rarely truly "need" them. The tools have shifted from essential equipment used by Garrett in risk/reward scenarios that require inventory economising, to high reward low risk tools that are easy to resupply. I didn't make my way through half the game without using water arrows because I felt I needed to economise them. I did so because I never felt the need to use them.
Do the difficulty modifiers help to enhance the game further? Is there a specific configuration of modifiers that help to recreate the classic Thief experience or make the game interesting?
Yes. I advise everybody proficient with stealth games to play on Master Custom, where the AI is more alert and deals the most damage, but not so much that it's cheap. Under the custom option lock off focus (super powered ability, not needed at all). You can also try turning on "stealth takedowns only" disables vertical takedowns and requires AI not be in an alert state, which will lessen the easiness of blackjacking. You may also turn on other options, like more expensive resources and slower movement. I didn't, but in retrospect maybe should have.
You can turn on/off almost everything related to the hud. I advise turning off waypoint markers to make level exploration more interesting. Turning off guard status display also demands you pay more attention to their stance/audio.