Yea, NatGeo asked me to hold fort while he's away, so I'll keep this project going :)
With our current line-up here are the major threats:
Drought - NWO is spot on that this team loses against Sun teams. Nothing but Rotom-W has a chance at surviving Sun-boosted onslaught from sweepers like Scarf Darmanitan, Volcarona, and Heatran. Rotom-W can only deal with one Fire mon before the second Fire-type plows through the team. 
Grass-types - These includes Chlorophyll Sweepers from Sun teams, as nothing on the team survives Grass + Fire offense. The good thing about this team, is that Thunder Wave on Jirachi and Rotom-W prevents Chloro and Fire-type Sweepers from setting up. However, Sleep Powder Venusaur and Nasty Plot Celebi are still gonna disrupt this team. 
Fighting-types - No reliable Fighting-resist means that Pokemon like Terrakion and Mienshao can simply spam their powerful STAB move and kill something. 
Heavy Offense - After the loss of Deoxys-S, Heavy Offense has become less prominent, but they still exist, with Pokemon like Espeon to fill in Deoxys-S's void. Haxorus, Dragonite, and SD Scizor would be hard to break with this team. 
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Heavy Offense, Fire-types, and Fighting-types can be checked with physically-bulky Gyarados. Intimidate neuters Physical Sweepers and Dragon Tail / Thunder Wave disrupts set-up. Gyarados and Jirachi together puts a solid plug on Dragon Dancers. Gyarados not only provides a solid physical defense and key resistances that this team lacks, but also provides paralysis support to this relatively slow team. As Birkal mentioned, although Gyarados is SR-weak, combined with its complementary defense with Jirachi, it easily receives Wishes. 
Gyarados @ Leftovers
Trait: Intimidate
EVs: 252 HP / 248 Def / 8 SpD
Impish Nature (+Def, -SpA)
- Waterfall
- Dragon Tail
- Thunder Wave
- Taunt
Scizor provides further check to Fighting- and Dragon-types, as well as providing a check to Grass-type Sweepers, with its powerful Bullet Punch. 
Scizor @ Life Orb 
Trait: Technician
EVs: 4 HP / 252 Atk / 252 Spe
Jolly Nature (+Spe, -SpA)
- Bullet Punch
- Bug Bite 
- Superpower
- Swords Dance
Jolly has some perks, such as outrunning usual Scizor counters like Calm Heatran, Magnezone, non-choiced Rotom-W, and taking them out before they can retaliate. It also has a nice perk of being faster than most Stallbreaker Mew, allowing it to pick off Mew before getting burned. Scizor provides some nice Steel-type breaking power to aid in Virizion's sweep.