New late-game strat for Emerald

+16 seconds to get desert candy
+4 seconds of YOLO grass on Route 110
-3 seconds on Timmy because repel wears off on tile before him
+3.5 seconds to use candy
TOTAL: +20.5 seconds

+18.5 seconds to get lake candy
+3 seconds of YOLO water/grass
+3.5 seconds to use candy
TOTAL: +25 seconds

+4.5 seconds to try to learn Protect (only if both candies are used)

1 CANDY: +20.5 seconds
2 CANDIES: +50 seconds

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Get the desert, Petalburg and Mt. Pyre candies. Make sure you have at least 1 Revive. Use the candies atop Mt. Pyre to reach Lv. 37, and equip Mystic Water. Keep Swampert in slot 1. Do the Fortree Gym double battle as normal. If you're in Torrent, heal only Castform before the Tropius fight. If you're not in Torrent, heal Swampert to an HP at which 1 non-crit Razor Leaf puts you in Torrent. Keep Swampert in until it's in Torrent, then switch to Castform and spam Powder Snow. If Swampert dies to a crit, Revive it before Winona and use old strats (1 X Attack).

Assuming you're in Torrent for Winona, the fight should go like this:
Turn 1: X Attack (anything but Perish Song)
Turn 2: Strength or Surf
Turn 3: Strength
Turn 4: Strength
Turn 5: X Attack (Pelipper will protect)
Turn 6: X Attack (Pelipper will protect)
Turn 7: X Attack (Pelipper will protect)
Turn 8: Rock Tomb (Pelipper will protect)
Turn 9: Strength
Turn 10: Surf
Turn 11: Strength

The only risks are Perish Song, which is only a time loss if you have 1 spare X Attack; Protect, which is only a time loss; and critical Aerial Ace, which is about 1/100 and doesn't always kill. You can always use an Oran Berry or Potion before Winona to reach high Torrent. Any runnable stats are guaranteed to 2HKO Tropius and OHKO everything else. If Swablu uses Perish Song, switch to a slave after the first Strength on Tropius, let it die, then switch to Swampert and spam X Attacks on Tropius until it charges Solarbeam (it often uses Synthesis first).

Leading with Swampert against Tropius loses about 10 seconds by itself, but it yields the following benefits:
- Don't have to switch Castform to slot 1 (-1.8 seconds)
- Don't have to switch Swampert back to slot 1 (~4 seconds)
- Swampert gets Lv. 43 for Lunatone, which allows a strat on T&L that's 25-40 seconds faster, assuming 23+ IV neutral Sp. Atk
- Castform never reaches Lv. 28 (~3 seconds)

The extra experience from the desert candy yields the following benefits:
- Lv. 37 for Fortree Gym double battle (slightly improved everything)
- More consistent Winona fight
- More consistent Torrent for Maxie/Matt
- Lv. 40 for Mightyena (very relevant with bad Sp. Atk or Speed, otherwise irrelevant)
- Lv. 40 for Crobat (saves a Super Potion turn + can help tank a Wing Attack)
- Lv. 41 for Golbat (very relevant with bad Sp. Atk or Speed, otherwise irrelevant)
- Lv. 41 for Gyarados (might allow Strength over Rock Tomb)
- Lv. 42 for Xatu (easier 2HKO with fast strat + less likely to enter Psychic range)
- Lv. 44 for true double battle (slightly improved everything)
- Lv. 45 for Crobat (can help outspeed at +1)
- Lv. 45 for Sharpedo (easier OHKO at +1 with Torrented Surf)

This is the standard fast strat for T&L:
Turn 1: X Speed, switch to Poochyena
(Poochyena dies, send out Castform)
Turn 2: X Special, switch to Taillow
(Taillow dies, send out Abra)
(Abra dies, send out Castform)
Turn 3: Surf, Powder Snow
(Castform dies)
Turn 4: Surf
Turn 5: Surf

An even faster T&L strat can be found here: http://pastebin.com/H5PbS7VN. This one requires specific stats and better luck (EQ+EQ+Ancientpower must put you in Torrent, but EQ+EQ+Xatu Psychic must be unable to kill).

Assuming 31/31/31/31/31/31 IVs and a neutral nature, here is a rough estimate of the average time saves/gains:
+20.5 seconds for desert candy
-1 second on Fortree Gym double battle
+1.2 seconds on Tropius battle
-12 seconds on Winona (support notes: http://pastebin.com/iBhPqbfm)
-6 seconds on Maxie 2
-1 second on Gyarados
-25 seconds on T&L
-1 second on true double battle
-1 second on Archie
TOTAL: -25.3 seconds