Warning of potentially gamebreaking glitch received from a user: 

I'm going to start this off by stating the most obvious, but most important, tip I can give you: SAVE YOUR GAME OFTEN. I sometimes will point out specific spots to save, but the more often you save when you haven't made any mistakes, the less time you will spend replaying areas.

If you know you haven't been spotted, and you've gotten all the collectibles and whatnot, or are working on a speedrun having gone particularly speedily, SAVE YOUR GAME. If you're trying a difficult jump, SAVE YOUR GAME. If you're about to attempt to cross a room with several patrolling guards and aren't 100% confident of the path, or even if you are, SAVE YOUR GAME. This will save you tons of time replaying areas if you mess something up.

Play on Easy difficulty. There are no difficulty-related achievements.

Most of the guards in the game are either stationary (unless they spot you), or follow a very defined patrol pattern. When you're in a safe spot, you can sit and watch their paths indefinitely to get an idea on the best timing and route to traverse an area. The levels are very open, providing numerous routes for you to take to reach the waypoints. I'll provide one route, but remember that if you alert a guard or don't have the timing close enough to my timing in the guide, you may have to ad-lib your path a little from time to time.

Skills: The most important skills to purchase are the stealth tree (all of it) and the agility ability for quiet landings, and the equipment tree. After that, focus on the clone tree. Once those are done, purchase the first two skills in the kill tree, because the latter missions will have you killing goblins, which don't count against Mercy, and the kill tree will help with that. Here's an abbreviated roadmap for those that would like to go through the game without a step-by-step guide for their first run or two.

Playthrough 1 - Ghost, Mercy, & Thief Insignias on every mission (No Alerts, No Kills, All Tokens and Relics)

• After Mission 0 (Reminiscences), you should have enough points to purchase the first 3 Stealth skills and the Silent Landing skill under Agility
• After Mission 1 (Akenash's Atrium), purchase the final Stealth skill and begin working on the Equipment tree (more health vials, acid, and daggers). If you have enough points left, since you can't buy the final Equipment skill, purchase the first Amber Vision skill.
• After Mission 2 (Master Key), purchase the final Equipment skill (3 amber vials), buy the first two skills in the Cloning and Kill trees (so that you have Aerial Kill)
• After Mission 3 (Deliverance), finish the Cloning Tree, buy the first Amber Vision skill, any extra in Agility.
• After Mission 4 (The Creator), finish the Agility Tree, save any extra points.
• After Mission 5 (The Architect), you should have Stealth, Cloning, Agility, and Equipment maxed out, and have the first two skills in the Kill tree so that you have Aerial Kills unlocked by now. Buy the ability in the Predator set that fully refills your life/amber when you drink a vial (Master of Vials?). Any remaining points can be put into the Amber Vision skills.
• After Mission 6 (Conflagration), finish off Amber Vision skills next. It doesn't matter what you buy at this point as all the crucial stuff is covered. Your next Predator skill should be Omniscience.

Playthrough 2 - Swiftness - Just replay each mission and head straight to the waypoint. You can ignore guards somewhat, although they may kill you if you're not at least a little careful. You should have no problem doing the Switfness Insignias provided you're not worrying about Tokens or secondary objectives.

Purchase all remaining skills after Playthrough 2, then just grind out all the cumulative achievements at whichever Mission/Checkpoint/Manual Save you wish, since they're all achievement tracker % based and not related to finishing missions.

Controls:

Press B to toggle sneak on. You'll be using sneak 99% of the time on playthrough 1.

Press RB to dodge roll, and RT to take cover against walls/boxes. Taking cover is especially useful at having guards walk right by you.

Use  and  to cycle through vials of life, vials of amber, throwing daggers, and sand. Use LB  to activate the currently-chosen item.

Hold LT and tap A to create a clone (same buttons to switch to controlling the clone).

Hold LT and tap X to activate invisibility. It runs out on its own. If you purchase the ability that gives infinite invisibility when standing still, you'll have to move to make it run out, although that isn't necessary.

When you have a clone out, hold LT and tap B to make it self-destruct, restoring some amber.

Hold LT and tap Y to activate amber vision. Once upgraded, this will show collectibles (Tokens), and further upgrades will allow you to see through walls, see guards' direction, etc.

The left thumbstick is for movement; right thumbstick for camera control. A  is jump. Holding it when jumping up to a ledge will cause you to hang from the ledge, otherwise you'll climb up automatically. This is important when avoiding guards patrolling above you.

will make Styx whistle, and a clone growl. This is used a few places in my WT, but can be used anywhere to lure guards away from their assigned station or patrol.

Lastly, don't worry if guards spot you. As long as they only turn yellow/orange on their alert status, you're fine and Ghost hasn't been negated. If they turn red, however, you'll need to load your most recent save/checkpoint. If they spot a CLONE and turn red, it does NOT void Ghost.

ONE FINAL NOTE: If you dont care about the completion and can skip the achievement for buying all skills, just play through the game in whatever manner you wish. You only need to max out the Clone tree and buy the first two skills in the Kill tree to get every achievement in the game except for the 'all skills' one in a single, unassisted playthrough. It should only take six hours or so to get 32/33 achievements in this manner. Only completionists or huge fans of the game need to spend another 20+ hours to get that last achievement.