So, to put it shortly, I've never seen anything like Mugen's priority system in real games, and I believe I've just about checked all the series that matter the most... whether one of the attacks wins or both chars hit each other is always decided based on the criteria I listed on the second quote.

Mugen-wise, that means using "Priority = 4, Hit" on all attacks, and by extension "Priority = 1, Miss" on all throws (although these would need some extra coding in the case of Capcom chars). Projectiles can have whatever you want AFAIK, though I always use 7.
So I'm surprised that even accuracy freaks use awesome stuff like priority 7, the highest, on weak normal attacks. +

For all this time, my general rule was assigning higher priority values for weaker attacks; the logic behind that was exactly:

Quote

The hitting portion of the animation comes out quick enough (many attacks actually only hit a tick or two after the char has reached the animation frame that appears to hit)

Triggers
Triggers are largely reliable when you are generally coding, but they can encounter problems when you are coding in specifically for CLSN Attack activation for the hitdef. Juggling in particular holds this problem up front and center.
There are many times where I have realized, that a ton of the things I was absolutely coding for in the hitdef, weren't activating properly (I.E. Time = 1; Time = 0; or an animelem that lasted for less than 2 ticks). If you place the CLSN Attack in an animation, where the attacking frame only lasts for 1 tick, or else directly code the hitdef to activate within 1 tick (i.e. time = 6), then only sometimes, you will notice, that the hit will not make contact . If you're not going for accuracy, or whatever, code it for something that activates for a period of 4 ticks, thereby increasing your chances of having the attack properly activate and connect with the opponent.
Movehit activation within specific animelems can also be a pain in certain cases. If that animelem lasts for less than 2 or 3 ticks, quite frequently you'll notice that the char won't activate the hitdef that you defined, meaning, again, that it will not make contact. Make sure the animelem lasts for maybe 3 or more ticks, or else code for more than one animelem.

For all this time, my general rule was assigning higher priority values for weaker attacks; the logic behind that was exactly:

Quote

The hitting portion of the animation comes out quick enough (many attacks actually only hit a tick or two after the char has reached the animation frame that appears to hit)

Quote

Yes there is a CLSN Attack Activation Glitch, but that's just something we have to deal with.

Man, you keep pulling all these glitches out of nowhere.

For all this time, my general rule was assigning higher priority values for weaker attacks; the logic behind that was exactly:

Quote

The hitting portion of the animation comes out quick enough (many attacks actually only hit a tick or two after the char has reached the animation frame that appears to hit)

Normally, weaker attacks are faster than stronger ones.

To support P.o.t.S.' position, I throw some more facts.
KOF 2002

KOF 97

(Here Daimon's attack is very quick so it seems that it has more priority)

SNK vs CAPCOM

(Ken's shoryuken has 9 frames of invulnerability, i.e. it has no CLSN2 box. That's why it beats other attacks)

Mugen-wise, that means using "Priority = 4, Hit" on all attacks, and by extension "Priority = 1, Miss" on all throws (although these would need some extra coding in the case of Capcom chars). Projectiles can have whatever you want AFAIK, though I always use 7.
So I'm surprised that even accuracy freaks use awesome stuff like priority 7, the highest, on weak normal attacks. +

i hate how kof sometimes won't show the clsn1 on certain ticks of certain attacks >.<.

Let's take Kyo's Hatsugane throw as example (with strong kick).
CMD:
[State -1, Hatsugane]; close to opponent, f + B or b + B
type = ChangeState
value = 850
triggerall = !var(0)
triggerall = ctrl
triggerall = StateType != A
triggerall = P2MoveType != H
triggerall = P2StateType = S || P2StateType = C
triggerall = P2BodyDist X = [-(const(size.ground.front)+const(size.ground.back)),0]
trigger1 = Helper(52087),var(2) && (Helper(52087),var(11) || Helper(52087),var(12))
CNS:
;-------------------------------------------------------------------------------
;------------------------------- Hatsugane Throw -------------------------------
;-------------------------------------------------------------------------------
[Statedef 850]
type = S
physics = S
movetype = A
anim = 850
ctrl = 0
velset = 0,0
facep2 = 1

[State a]
type = VarSet
trigger1 = !Time
var(3) = 0

[State a]
type = VarSet
trigger1 = !Time
trigger1 = command = "holdfwd"
var(3) = 1

[State a]
type = VarSet
trigger1 = !Time
trigger1 = command = "holdback"
var(3) = -1

[State b]
type = PosSet
trigger1 = !Time && Pos Y != 0
y = 0

[State 850, NotHitBy]
type = NotHitBy
trigger1 = !Time
IgnoreHitPause = 1
value = SCA
time = 1

[State 850, HitDef]
type = HitDef
trigger1 = 1
ID = 850
attr = S, NT
hitflag = M-
guardflag =
animtype = Light
guard.type = None
sparkno = S8060
guard.sparkno = -1
sparkxy = -20,-84
hitsound = S800,0
guardsound = -1
P2Facing = ifelse(ceil(P2Dist X)<0,-1,1)
hitonce = 1
numhits = 0

[State 850, ChangeState to Kick]
type = ChangeState
trigger1 = Time = 1
trigger1 = !MoveHit
IgnoreHitPause = 1
Persistent = 0
value = 240

[State 850, TargetState]
type = TargetState
trigger1 = Time = 1
trigger1 = MoveHit
IgnoreHitPause = 1
Persistent = 0
value = 852

[State 850, ChangeState to Throw]
type = ChangeState
trigger1 = Time = 1
trigger1 = MoveHit
IgnoreHitPause = 1
Persistent = 0
value = 851
AIR (one frame with duration 1):


Basically, throw triggers under the conditions described in CMD (note P2BodyDist X), then the first element of a close standing kick appears. If the hit occurs (meaning your opponent is not invincible) then the throw is succesful, if the hit misses then Kyo continues to close standing kick:
[State 240, ChangeAnim]
type = ChangeAnim
trigger1 = !Time
trigger1 = PrevStateNo = 850
value = 245
elem = 2

Personally, I see no meaning in using 1, Miss for throws as well.

Using 7, Hit for projectiles is not the right thing to do, in my opinion.

i got "proved wrong" for saying the same thing about one year ago  .. or something like that (maybe pots remembers that), so i stopped telling people about it. i also use priority = 4 for everithing, though i tweak my throws in a different way. and dman, i hate how kof sometimes won't show the clsn1 on certain ticks of certain attacks >.<.

I think throws have more "priority" over other attacks here, though I need to make some tests in KOF yet. Do you remember how P1 is invincible to projectile when P2 is grabbed (if projectile was fired at the same tick when P1's grab frame has appeared)? I used NotHitBy trigger at Time = 0 for this.