Chaos problems (spoilersish)

Don't forget folks, aside from save scumming (which I will admit I did in my first stealth/non-lethal type playthrough, I know I am filth >_< I blame OCD as well!), you have lots of tactics to use to get away, should you be spotted. You don't actually HAVE TO go on a massacre once you're spotted. Though it is equally fun, if not more, than a quick disappearing act sometimes >_>

But anywho, don't forget you can always -

*Blink away to high ground/shadows for a quick escape. Like some mentioned, there's almost always an escape option given how most of the areas have been designed. Look up and look around. Take your time to scout areas before you make your moves, ideally plotting escape routes should things go awry.

*Use combat sleep dart, once purchased, to put people down fast, especially in conjunction with the Bend Time ability.

*Or just use Bend Time to slow/freeze time and punk out easily, especially with Blinking. Don't be too stingy with mana potions, they're everywhere and cheap to restock in-between missions.

*Use the first rank of Wind Blast to knock people on their asses and retreat. I wouldn't risk rank 2, as you may splatter guys against walls. Also have to watch out for environmental hazards, like tossing people off ledges or into water or into that reprogrammed Wall of Light (many lulz and one of my favorite ways to pwn guards)

*Use Possession, rank 1 to jump into a nearby fish/dog/rat to avoid immediate assault (situational, I know), or much better, use rank 2 to jump into an aggro'd guard and walk off into another room or back-alley.

*Oh, and also, run away, duh :p

I also realize that once you're spotted, yes, the A.I. is a b**** to sneak around sometimes, and with the added heat of an alarm or lots of guards in cramped spaces, your options can be pretty limited. This is especially the case on Very Hard. Their sight ranges are ridiculous sometimes and they can be relentless once you're detected. Knowing the maps and being careful with how you move, using Blink and other abilities like Dark Vision and Possession to bypass patrols, pays dividends if you don't want to save scum. Take it nice and slow, no rush, and always favor high spots and dark areas. And like someone also said, don't forget you can opt to choke out that one nuisance guard that's in the way. Just be sure to carefully hide his body away from others so as to not draw the hate you're obviously trying to avoid in the first place.

I guess my main point though is that I would encourage people to not save scum, at least maybe not after your first playthrough and you've learned the maps and the gameplay a bit more, since really the experience of escaping is honestly so much fun in this game. With a game so heavily centered on consequence, I would say live with those consequences and just try to enjoy the flow of the game. You have tons of options to get away from encounters just as you do to finish them, and it seriously makes me feel like a gangster mofo pulling ninja vanish on a group of guards, even if they did spot me dropping down to knife their buddy on patrol. My 2 tl/dr cents. :3
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XBL GT- Sadist Mask
Wii FC - 0602-6131-7882

No problem
I generally focus on mobility in the early game too, especially if I'm aimed on using stealth over (or for) violence. Blink rank 2 is just too damn good, and being able to jump higher and move faster is uber, especially in conjunction with Blink maxed out. Lethal or not, it's really hard to argue against taking them over other stuff first. You can cover more ground, faster, and get to places more easily or that you couldn't in the first place. It's practically a MUST for sneaking, unless you want to be spamming the other abilities and using mana pots a lot.
Then again, yeah, Bend Time is so OP when used in the right situations, offensively and defensively, and Possession is great for stealth, infiltrating areas, and retreating. They're just so damn expensive ruin-wise >_< Mana-wise too! Which is definitely something to consider if you're going to take them early game and have them be your primary abilities.

If you're playing stealthily but also being fairly indiscriminate with killing (which I guess you wouldn't on a Low Chaos playthrough, but still...), I bet you will miss Shadow Kill as well. Luckily it's cheaper and much more accessible early game than maxed out Possession or Bend Time, and I feel like rank 2 isn't really that necessary as rank 1 is for avoiding detections and alerts.

The game really makes you choose your abilities carefully, I think, and ultimately that will determine how you play those first few levels until you have access to more options and abilities. In a way I think it makes the earlier missions harder, especially if it's your first playthrough and you don't have experience with the maps and guard/item placement. But hey, it also makes it all the more awesome later on when you have all those abilities and you feel so damn powerful! Plus, the end missions just keep getting crazier and crazier (assassins and Tallboys, oh my!) so I guess in a way it balances out.
Or maybe not...you can be pretty godly by endgame >_>

I feel you on Weepers and rat swarms possibly making your life more difficult, though. Rat swarms are a pain in the ass, because I'd say your best bet to dealing with them (aside from just avoiding them :p) is to pull out the pistol or toss a grenade/place a spring razor in retreat, and that is likely going to draw attention to yourself, the last thing you'll probably want if you are aiming for stealth and Low Chaos. Weepers I would recommend considering combat sleep dart and taking them out from afar if possible with darts (remember to stay stocked in-between missions! They seem to be pretty rare otherwise), if you can't off them due to your Chaos level goals. In groups they just suck to take down without lethal force. Sneaking, choking out lone Weepers, and high ground are obviously options for most Weepers and rat swarms and although they have much gimper detection ability than most other enemies, there are some areas late game, where yeah, dealing with them in tight spaces and large groups does just suck. Some parts of the Flooded District mission are what come to mind mostly. Really hard for me to not just whip out my pistol and blast them as they charge me zombie style, or bust out some Wind Blast and paint the walls their diseased asses xD
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XBL GT- Sadist Mask
Wii FC - 0602-6131-7882