disclaimer: a lot of these stuff can be yoloscrolled/swapped, but some of them can be quite risky since the lag from glitchy items can throw off your visual cues. The only mandatory yoloswap in my opinion is presurge elixir/soda pop swap

mart: 7xpokeballs, duble input escape rope, fast scroll to antidote, buffer A potion, fast scroll to awakening, buffer down+a burn heal, fast scroll paralyze heal 
cave: buffer slot2 escape rope (slot 3 if didnt buy antidote, slot4 if picked up potion and didnt use it aswell)

post missingno2: 
underflow,
buffer select slot 2, 
scroll down

jx[3]
jx[0]
masterballs <-- swap this

double input up to jx[3], throw 1

post charizard:
swap charizard in front
throw slot1, throw slot2 x6 times
double input select slot3
scroll down

jx[0]
ultraball
cancelx[5] <-- swap this

quad input to tm27, throw 14 
down select jx[0]
scroll down

paralyze heal
????????
ultra ball <-- swap this

yellow double input select hm04
yellow double input swap master ballx0
triple input select tm52
triple input swap burn heal
throw 19 tm52
scroll down

hp up
[][]G[]
jx[3] <-- select this

double input up swap with hp up
throw 8 j
walk one up, face down

post giovanni:
buffer down select slot 2 paralyze heal
scroll down

jx[0]
jx[0]
elixir <-- swap this (careful with yolo swap, if you swap the item below elixir it'll merge and you cant recover)

quad input select gary
scroll down

paralyze heal
?????????
ultra ball <-- swap this

select gary again
scroll down

tm37
nickname?
jx[5] <-- swap this

double input up select tm37, 
scroll up

tm27 <-- swap this
ultra ball
jx[2]

talk to giovanni, deposit everything but zard

post pc deposit:
triple input up paralyze heal 
scroll down

jx[5]
bike voucher
hm05 <-- swap this

close menu, walk 1 down 1 up
buffer A toss tm01 x[3]
down select buffer tm47
triple input up swap ultraball
face right

(slash arcanine)
post blaine:
select slot1
scroll down

ultraball x0
glitchy mess
tm01 x3 <-- swap this

double input select hm04
down swap potion
up buffer throw 15 potion (from the top)
up buffer throw x[0] ultraball
up select master balls
scroll down

[][]I[]
EXP ALL
jx[5] <-- swap this

yellow double input select tm32
triple input swap [][]G[]
throw x[4]tm32
quad input select moon stones

scroll up

jx[5] <-- swap this
tm32
cancel

throw x[9] moon stones

walk 2 up, 1 down, turn up

post sabrina:
walk down, slot 2 elixir, slot 3 cancel to koga

post koga:
triple input select paralyze heal, 
scroll down

jx[0]
jx[1]
silph scope <-- swap this

buffer throw x[0] paralyze heals
yellow double input select cancel
scroll down

ultra ballx0
[]Q[]r[][]4[]h
hm04 <--swap this

select cancel again, double input swap up ultra ball
select cancel again, 
scroll down

tm14
lemonade
jx[5] <-- swap this

scroll up

jx[7] <-- scroll until here
potion
pokedex

walk up one

buffer throw 2 jx[7]

up select antidote
up select swap pokeball
throw x[2] antidote
talk to erika

post erika: 
walk down
buffer down select slot 2 elixir
scroll down

jx[0]
jx[1]
soda pop <-- yoloswap this, keep fast scrolling

tm48
paralyze heal
????????? <-- use this
enter surge gym, walk one up

down select ultra ball
yellow double input swap hm04
up A buffer 7f, throw 5
yellow double input throw x[3] pokeball
down A jx[5], throw 2 (careful of input lag, can easily crash the game)
walk one down, face surge on the right

post surge:

walk one down, one right, keep holding down, enter misty gym
double input use cancel
(rage starmie)

post misty:
down select buffer slot 2 soda pop, 
scroll down

hm04
great ballx0
masterballx3 <-- swap this 

double input up select hm04,
buffer down swap, 
scroll down 

potion
???????
[][][][]m[]x72 <-- select this (check is this a quad input?)

triple input swap jx[5]
throw 18 [][][][]m[]x72
close the menu with up buffer
walk one up
triple input up select ????? (quad input if you didnt close the menu with up buffer)

triple input up swap [][]G[]
double input select potion
triple input up swap hm05
throw 6 potion (from top)
up a throw x[2] max revives
walk left to bruno

post bruno:
walk down