[Rewriting in progress; some inconsistencies may be present.]

I had been trying out some variations of PP Up strats on my runs, but they
didn't always seem like a net win. Then Exarion independently worked out a
few things, and there are some times (usually involving not-quite-as-good
Attack) where it's definitely worth it. The routing explained here is
a mixture of what used to be here and of his flavor of PP Up strats,
so it's not completely optimized. Here's what to do differently:

Defer selling things off until the Celadon Department Store. This is
because we're getting the second Nugget. Time cost: 6 bike steps, 1
hidden item jingle, any extra time needed to hunt around for the Nugget
if you're not exactly sure where it is.

Buy 2 additional X Accuracy. Time cost: two button presses.

(Since you have at least ¥3100 extra to throw around even with this,
you could buy yet another and/or some extra X Speed as insurance against
Agatha's Golbat pulling off Haze.)

On Cycling Road, get the hidden PP Up. When hugging the right wall after
the grass patch, it's on the upper right tile of the seventh row of
flowers below the Biker you pass in the next column. You can stay in that
column the rest of the way down - the remaining Biker has insufficient
visual range to see you - so there's no extra movement. Time cost:
one hidden item jingle.

After gatehouse when entering Fuchsia, use the PP Up on Nidoking's Horn
Drill. Cursor goes to top of item menu; use bike. Time cost: scrolling
down to PP Up, using it.

Rocket with Machoke on Silph 10F: xacc, drill. Time cost: using xacc. Time
savings: one less Machoke turn, two less Nidoking attack turns, quick
Horn Drill animation instead of longer first-turn Thrash one.

Last Juggler before Koga: xacc, drill, drill. Time cost: using xacc,
and Drowzee gets a turn. (Danger: it has Psychic! Have plenty of HP going
into this! Not counting this against time since the usual route uses some
healing items before this battle anyway because oneshotting the Hypno
is unlikely.) Time savings: two Earthquake animations replaced with Horn
Drill ones, and you oneshot the Hypno, which otherwise requires a crit.

(With boom strats, only 3 drills are used on Koga, and none are used
between then and the next Elixir point, so this strategy could be used
even without the PP Up as long as you have an extra X Accuracy for
it. This also means that if you happen to be deep enough in redbar when
you get to Koga's Weezing, you can just drill it too with the sixth PP
to get the battle over much faster and still be in redbar after all of
the ensuing Rare Candying.)

Indigo Pokémon Center: despite drilling Viridian Rival's Venusaur,
you still have 5 drills left to sweep Lorelei in the usual manner, so
you can center skip without having to worry about whether you have good
enough Attack to reliably oneshot Jynx with Earthquake. Plus, quicker
animation, and you can just mash A through the battle like usual.

(When center skipping, don't forget to swap the E4 Elixir/Ether usage!)

Bruno: Could drill the second Onix since you have an extra PP. Depends
whether the time for "It's not very effective..." would outweigh how long
it personally takes you to move the attack cursor to Ice Beam and back.

Champion: xspeed, xacc, drill x6. Full animations are forced on for this
battle, so the time saved due to Horn Drill over Earthquake is much more
significant. Plus, once everything is set up, you get to just mindlessly
mash A until the game is finished.

Also, if some mishap happens with XP routing post-Mansion (the last place
Rare Candies are used, so the last synchronization point for XP routing),
you don't have to worry about losing your stacked badge boost on Attack
(and the consequent risk of Earthquake not oneshotting the Alakazam)
in the event that you level off of the Pidgeot. This once happened
to me when I found myself with an extra Rare Candy at the Mansion and
foolishly used it anyway - Nidoking leveled on Pidgeot, and Earthquake
left Alakazam with 1 HP, allowing it to Psybeam me to death.

Routing considerations with the PP Up: Obviously, you now have a sixth
Horn Drill in between Elixirs/Ethers/centers; use it well. When a PP Up
is used on a move, the boost in max PP is also applied to current PP,
so for menu optimization purposes, use of the PP Up could be deferred to
anywhere before Giovanni I, as that's the first place that a sixth Horn
Drill is used. But since HM03 fills up your inventory, in the current
routing the PP Up must be used before that. I put the use of it in a
place I thought looked good; I don't see a better one.

Due to the extra money left over, I thought about the possibility of
additional xacc+drill usage on any trainer whose Pokémon we're not
guaranteed (modulo gen1-missing) to oneshot all of. Here's why not to
for each:

Blaine: Seems a bit slower, but if you don't feel like chancing Arcanine's
damage range, you can xacc on Growlithe (which will always use Agility),
quake, quake, quake, drill. Take Down and Fire Blast really hurt, and
you'll be very sad if you get burned, so you may find this to be worth it
on subpar Attack. Time cost: using xacc, Growlithe using Agility twice
(since it outspeeds you the second time). Time savings: Horn Drill
animation instead of Earthquake, guaranteed oneshot of Arcanine.

Karate King (last trainer before Giovanni II): The drill PP needed for
that would be better used to allow the Indigo center skip, and you take
the potential hit from the first Machoke anyway that you'd also get with
the usual X Special strategy. (But you could get and use the Max Ether
on the way up Route 23...)

Giovanni II: The Rhydon will only ever use Fissure, which can never hit
you (as you outspeed it), so the fact that it takes two Ice Beams does not
put you in danger. Also, you'd then arrive at Lorelei with only 4 drill
PP, necessitating good enough Attack to oneshot Jynx with Earthquake,
defeating the purpose of these strats.

Lance: A first-turn oneshot of Gyarados can only happen with a crit
Thunderbolt or a yolodrill. If your Special hasn't been increased by at
least one stage when Gyarados gets a turn, Hydro Pump kills you outright,
even without critting. The only reasonable first action is using an X
Special (and therefore oneshotting with Thunderbolt next turn), at which
point you may as well use the usual strategy. The subsequent X Speed
would be required anyway to outspeed Aerodactyl, and on good special
it's a guaranteed (modulo gen1-missing) oneshot too.