That's still good progress. :P
If you are hatching a flawless baby missing the shininess, that means the wandering offscreen trainers are secretly advancing the PID RNG (controls shininiess) Frame. Shame you can't rebattle the trainers and unleash your level 100 Arceus on them, huh ?
1) wrong nature, wrong IVs, not shiny
Reset and try again. It's only a Weedle so it should only take a few minutes to hatch. If you're hatching something like Larvesta with base 10,000 steps, there is a shortcut to determine whether or not the baby is flawless.
2) wrong nature, flawless, not shiny
3) right nature, flawless, not shiny
Good, but not quite the right PID. You'll have to pull up a table of the natures after your intended target. You are most likely 1-5 PID frames too far ahead of the shiny.
Here's what you do:
Change Method to Breeding (BW) Method (or International if applicable to you).
Calculate the Starting Frame again.
Copy Paste Seed into Seed (Hex).
Uncheck the shiny box. Click Generate.
Examine the Natures of your generated table. You should have landed maybe 1-5 frames after your Target PIDRNG Frame.
If you hatch a Pokemon wrong nature, just match it on the table. If you hatch a Pokemon with the Everstone nature, you may have trouble matching it. Just do 1 less Chatter the next time until you happen to land on a wrong nature.
For example, I hatched a
Bashful Pokemon, which happens to be on
Frame 57. I am trying to hit
Frame 53. 57-53=4. I need to do 4 less Chatter advancements in order to get that Calm Shiny Pokemon. On my next attempt, I will do 0 Chatter advancements.
This time, I successfully hatched a shiny Calm Pokemon.
In other words, if you got a "wrong nature, flawless, not shiny", you are very close to your shiny! Just do some math and figure out how far off in the Chatter advancements you were. o.0
Do NOT resave and do NOT keep the wrongegg+save. This is pointless. You'll change where the wandering trainers (i.e. NPCs) are turning/walking, thus throwing off the math again. Just soft reset if it is not shiny.
Of course, in my example, if my target is 53 and I consistently hatched a Jolly (Frame 59) egg, I would have to resave to change the position of the NPCs. They're messing up my PID by too many frames, or I just stink at button mashing to collect the egg. -_-