I was thinking it would say something like what is says on Lucario's analysis:
"Whether you choose an Modest (Adamant) or Timid (Jolly) nature depends on your team. Modest (Adamant) gets important OHKOs against Jirachi, Celebi and Shaymin (Bronzong and Skarmory), but a Timid (Jolly) nature allows Empoleon (Lucario) to outspeed important Scarf-ers such as positive natured Rotom-A, Heracross and Offensive Suicune that got Trick-ed a Scarf as well as neutral natured Flygon and Jirachi (Jolly Gyarados, Timid Suicune, and Timid Rotom-A)."
All of Which can potentially end your sweep.
Here are the calcs anyway though:
+1 Timid Torrent Surf at 252/0 Rotom-A
96.7% - 113.8%
+1 Timid Torrent Surf at 4/0 Flygon
123.9% - 145.8%
+1 Timid Torrent Surf at 4/0 Heracross
107.6% - 126.9%
+1 Timid Torrent Surf at 252/0 Machamp
93.2% - 109.9%
+1 Timid Torrent Surf at 216/56 Swampert
80.8% - 95.8%
+1 Timid Grass Knot at 136/0 Starmie
90.8% - 107.1%
So yeah, all of them will still die to your triple boosted Surfs after a switch-in to Stealth Rocks or something... Grass Knot may miss the OHKO on 252/0 Starmie even with Stealth Rocks however.
You also STILL 2HKO:
252/0 Suicune with Grass Knot
156/0 Gyarados with grass Knot
A little mention of the importance of Stealth Rocks when running Timid may need to be put in as well.The very slight added bulk can also help in a few places though I have yet to feel it tbh.. You could also just run max speed to outpace Jolly 252 EVs Breloom before an Agility. Basically what I'm trying to say is that Timid at least deserves a mention SOMEWHERE in Empoleon's entire analysis.
The loss in power affects things such as:
+1 Timid Torrent Surf at 4/0 Jirachi
91.2% - 107.3% (no OHKO even with a switchin to Stealth Rocks)
+1 Timid Ice Beam at 0/4 Shaymin
80.9% - 95.6% (Lose the guaranteed OHKO with Stealth Rocks, still kill him after a turn of Life Orb though so at least its a tie =\)
+1 Timid Ice Beam at 252/0 Celebi
68.8% - 81.2% (lose the small chance to OHKO with stealth rocks completely)
+1 Timid Ice Beam at 156/0 Gyarados
37.3% - 44.3% (small chance to miss the 2hko)