Whimsicott is perhaps one of the more overhyped Pokemon in early BW besides Haxorus, but quirky history aside, Whimsicott has proven itself to have a niche in just about any environment it's allowed in. It specifically differentiates itself from other Pokemon thanks to Prankster combined with a huge number of helpful and annoying support options, ranging from Encore to Taunt to Tailwind. This alone makes Whimsicott an ultimate annoyer and team supporter, capable of disrupting the opponent while creating switch-in and setup opportunities for your own Pokemon. While its ability to use Prankster effectively is awesome, Whimsicott itself is decidedly subpar; its bulk is mediocre and it lacks reliable recovery, and may become dead weight on teams due to a lack of offensive presence outside of Leech Seed, which isn't even a main option on this analysis. Additionally, because Whimsicott is notorious for what it does, it is somewhat predictable, and thus requires great patience and prediction to use. However, its presence causes a number of competent players to play cautiously around it, so they, too, are capable of serious mispredictions and ill-timed decisions. At the end of the day, be wary that Whimsicott is high-risk with unpredictable rewards.
The best set Whimsicott can pull off is pure utility and support, but this set is so well-known and stops so many otherwise dangerous Pokemon in their tracks that good players have to be prepared to face it at any given time. The purpose of this set is to throw off momentum and prevent possible setup with Encore and Taunt, then maintaining your own team's momentum (and possibly give free turns) by switching out or following up with a support move afterwards. It should be noted that even if the opponent has successfully predicted Whimsicott's actions and switched to another Pokemon, Whimsicott has essentially done its job at averting the opponent's original plans, and can also adapt around the situation if needed.
Tailwind and Stun Spore are supplementary support moves. The former temporarily boosts the Speed of teammates for a couple of turns, and is especially a good last resort option if ridiculously fast threats such as Chlorophyll Venusaur, Sand Rush Stoutland, Choice Scarf Salamence, and Choice Scarf Keldeo are terrorizing your team. Stun Spore is more useful for its Speed drop, which is especially useful for some troublesome targets such as paraflinch Jirachi or a Pokemon with too many Speed boosts. The scouting move of choice depends on preferences; U-turn is relatively standard and ensures Whimsicott won't die early early in the game, as it can support its team with Tailwind and Encore multiple times if needed. On the other hand, Memento creates setup opportunities for sweepers as it will likely force the opponent to switch out, although it will be harder to use Whimsicott and predict due to a lack of a reliable scouting move.Team Options & Additional Comments >>>
This is the part where you say "where's SubSeed?" Yes, while the combination of SubSeed and Prankster is extremely obvious on Whimsicott, it sadly needs tons of support in order to work, especially as Celebi, Heatran, and Magic Bounce users are common in the metagame. Additionally, using SubSeed requires a stressful level of prediction, and in general, you will find yourself wishing you had faster ways of overpowering the opposition. Outside of this, Whimsicott has tons of other support options to use with Prankster, though most of them are either unreliable or situational. Special mentions go to Cotton Guard, which boosts Whimsicott's physical defense to impenetrable levels but is badly checked by any powerful special attacker, Light Screen, which gives much-needed but short protection against special attacks, and GrassWhistle, which would be undisputedly be a good option if not for its unreliable accuracy. Trick Room is also decent on paper with U-turn, though keep in mind that Trick Room is not affected by Prankster, and that there are other Pokemon that can both sweep as well as set up Trick Room, unlike Whimsicott.
While Whimsicott's offensive movepool is actually quite nice, offensive options are also quite limited due to Whimsicott's low base 77 Special Attack stat, in addition to some attacks' conflicting reliance on weather (Hurricane versus Growth in rain or sun). Even with investment, it's not hitting very hard, so Venusaur and Celebi are more powerful and reliable alternatives. Speaking of which, Whimsicott can also use Sunny Day to change the weather in a pinch against opposing weather teams. However, Ninetales does this role simply by switching in, and other reliable Sunny Day users, such as Venusaur and Heatran, exist.
Checks and Counters
Although Whimsicott allows very little setup opportunities with Taunt and Encore (so one would be smart not to attempt to set up) and can choose to avoid confrontation via U-turn, just attacking it will do the trick because it has absolutely no offensive presence. Heatran, amongst many others, has absolutely little to no trouble with Whimsicott, as it doesn't mind paralysis much, and can simply spam Roar, Taunt, or its Fire-type moves if Taunted. Should Whimsicott choose to use Leech Seed, Grass-types such as Ferrothorn, Breloom, and Celebi can just switch in and attack. U-turn users such as Celebi, Scizor, and Landorus-T also do well in most cases, as U-turn naturally does heavy damage, and allows the opponent to adapt and predict around Whimsicott depending on the situation. Priority users also do decently well against Whimsicott, although there are actually very little in the metagame that can beat Whimsicott's priority moves besides Weavile's Ice Shard, Terrakion's Quick Attack, and Lucario and Dragonite's ExtremeSpeed. Even then, Whimsicott can survive a couple of hits from these attacks due to defensive investment, so it must be weakened beforehand.
There are also specific ways of beating Whimsicott. Opposing Prankster users tend to employ Taunt, which can potentially stop Whimsicott from functioning effectively. Only Tornadus and Liepard can do this in practice, however, as both invest heavily in speed and thus outrun Whimsicott naturally, while Prankster Sableye is too slow to use its own support moves against the threat of Whimsicott's faster Encore and Taunt. Whimsicott also despises Magic Bounce users, and although its simple solution is using U-turn, the Magic Bounce users can always switch back in and limit its actions. Whimsicott's lack of recovery and reliance on prediction are also crippling downfalls, as it switches in often and can easily be worn down by Spikes and Stealth Rock in addition to random or well-timed attacks.