A few quick thoughts and opinions, take it with a grain of salt…
What exactly are the Shadowthorne? How do they come to be? Is this a hand-picked Religious Order? Can any Elven rogue follow this path? When I read the description, it doesn’t leave me feeling any connection nr any point of reference to what the class “Is”.
Some mechanics points/questions…
Requirements:
* Why do you list both Evasion AND +3d6 Sneak Attack? By the time you get +3d6, you already have Evasion.
* Why require the Investigator feat? From what it appears, this class seems to be an Elven (Non-Evil) Assassin type. Doesn’t seem to be a fitting requirement. Or was it requisite to reach 3 feats to require 6th level before entry?
Skills:
* If this is a Rogue base, why the reduction in Skill Points to 4+?
With the BAB increases I can see lowering Skill Points, but I would think no more than to 6+. Class abilities are balanced overall for what you lose, again pointing to a lower decrease in SP.
Abilities:
Sudden Strike: Since this ability is giving the equivalent of a feat-like function, I would slightly change this. Since Improved Initiative grants +4 Initiative, and a feat like Blooded grants +2 Initiative and +2 Spot, I would alter this thusly.
Sudden Strike (Ex): A shadowthorne grows more skilled at striking without warning; as such the character gains a +2 bonus to initiative and a +2 bonus to bluff skill checks made to feint in combat. These bonus stack with bonuses gained from other sources such as the Improved Initiative or Skill Focus feats.
OR … to actually make this linked to the Focus Weapon.
Sudden Strike (Ex): A shadowthorne grows more skilled at striking without warning; as such the character gains a +4 bonus to initiative, but only with their signature weapon. This bonus stacks with the bonus gained from the Improved Initiative feat.
On another note, I would exchange Weapon Bond (1st) and Sudden Strike (3rd). Makes more logical sense that they would learn the bond with the weapon and the speed to draw it before learning the increased combat prowess.
Ranged Sneak: This applies to Ranged Sneak Attack damage I assume? If so you should state it explicitly, otherwise it could be surmised you are granting “reach” on sneak attacks.
Ranged Sneak (Ex): The range at which the extra damage from a ranged sneak attack can be applied is increased from the base 30’ range to 40’ at level 2. The range is further increased by another 10 feet at both levels 5 and 8.
Critical Strike: Why only by 1? Why not just grant the Improved Critical feat? Simpler and cleaner.
Ghost in the Wind & Whispers in the Wind: These are (IMHO) way too much. You are basically granting 8 Skill Focus feats here – that’s 8 feats over 4 levels. On top of it you are basically avoiding the restriction on Skill Focus that skill focus bonuses don’t stack on the same skill. Worse yet – you do not state that these DON’T stack with Skill Focus.
Skill Focus (Hide) x2
Skill Focus (Move Silent) x2
Skill Focus (Gather Information) x2
Skill Focus (Diplomacy) x2
This (again IMHO) really needs to be trimmed way down. Especially once you consider the epic levels which are handing out Skill Focus feats like candy.
Invisibility & Non-Detection: These work fine but I would alter the levels slightly, granting Invisibility 2 @ 7th. This keeps both iterations at +5 levels from the level originally gained, and prevents 3 abilities in one level.
Anyway, JMHO - Hope this helps.