Since you wanted to know how we see your ideas here's what I think about them. This is purely from a PvE pov since that's what i play 99% of the time.
Rage/Fury: Seems good, would be interesting to see if they'd implement new forms.
Madness: 20% healing is really strong. That's probably too much.
Hatred 1: Making CC relevant in a rotation isn't a good idea.
Hatred 2: Assuming you mean that the damage the charge deals heals for 15% this seems like an interesting idea.
Hatred 3: Reducing the maximum health of an op boss is just... wrong. Hatred would become way too strong. And a third dot isn't what this specc needs in my opinion.
Hatred 4: Way too much rng, too hard to balance.
Hatred 5: Same as Hatred 1
Darkness: Maybe too strong, 15% seems too much.
Carnage 1: I like this.
Carnage 2: Gapcloser in a rotation aren't a good idea either.
Marksmanship: Well ... The damage needs to be high enough to justify the 8sec cast time, so it'll be really strong, especially as an opener. But then you'll generate so much threat that every tank will hate you. And don't let me start about PvP...
Engineering: Seems like a really interesting ability. But on multi target encounters the damage may be too random. Maybe make it so that the probe attacks your main target or smt like that
Deception: I like the idea of this, if it works like retaliation (?) for juggernaut tanks.
Lightning: I don't play lightning but generally speaking I like it. Maybe make the damage high enough so it's viable to use on a single target (or implement proccs so it ticks faster etc). Otherwise I don't see a reason for changing force storm.
Concealment: If this is supposed to be a channeled attack I don't like it, because I feel it doesn't fit the play style. If it isn't I like it.
Arsenal Mercenary: Arsenal already has a filler ability, do I don't see a reason to give them a new one. And adding a cool down to this ability would probably defeat the purpose of replacing an ability without a cool down. Maybe you could use it as a filler for aoe situations (?).
Arsenal 2: This would probably look really awesome. Make it deal high enough damage to make it viable using on a single target and it's perfect.
AP PT 1&2: Again, gap closer shouldn't be used/needed in a single target scenario.
AP PT 3: Yeah why not. At least for PvE I don't see why they shouldn't get a proper execute.
AP PT 4: Take the discipline with the highest burst and add ... more burst? I can already see the tanks screaming in pain and the pvpers crying for nerfs.
Vengeance 1: Seems like a good idea.
Vengeance 2: During my last TFB run there was like one time where I was able to use retaliate. So for this to be viable you need some kind of procc so it's possible to use our without any restrictions.
Annihilation 1: I don't need to explain how op this would be, right?
Annihilation 2: This would be really useless in PvE. Too much rng and not enough occasions where you can use it.
That's what I think about your suggestions. While I really like the ideas behind most of them they are either to strong or kind of useless in PvE most of the time. But I'm not pro so I may have missed something.