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Well, the effects don't really apply. There's Sandstorm and hail that damage you overtime. Could be part of a specific area. If you try to cross it at the wrong time, or without a particular effect, you get damaged as you cross it, making it a challenge or an impossibility.
Could be applied to anything really. Sidetrack from weather a bit: Enviroment: Think of a cracked floor with lava showing in the cracks, or spikes all around it. Try to move around it, and you'll get damaged, bad. Only as you move in the spikes, and constantly whenever over lava. You can try to shrug it off, which could be done with pauses for healing rings in spikes, or loads of bandages and speeding rings over lava. Just to annoy you, there could be enemies that cause knock-back and sleep in those places respectively, forcing you to just LOVE iron will a bit more.

Then, back to pokemon, there's Sunny Day and Rain Dance... uh... Rainy Day, I guess. The effects boost and depower Fire and Water type moves respectively. I can only see this working if there were elemental rings.
Now, if elemental rings were added, these ones could work perfectly, and anywhere, to some area specific predetermined possible weathers. Some good and some bad, as they hurt or hlp you against animated.

And to the idea as a whole: I love it. I love the concept of animated coming at different times of the day already, making an enemy come out rarely during certain weather effects would be cool too.
For example, think that sometimes, maybe once every 4 gaia nights, Zen and Bassken would fall under a weather effect called 'River Mist', which makes the place seem more eerie. In Zen, you'd find all Taikus replaced by this and in Bassken, there'd be these near the lake's shores, which would be meant to be confused as related to Bassie.

z!deaaaaas...

Environmental damage (that is, damage from stuff that doesn't have a health bar): I always like the idea of environmental damage of any kind. There's lava (including rising lava), spikes (actually, I think the tactic would be loads of bandages without the speed rings - no matter how fast you go, you're still stepping over the same amount of spikes, so you're just speeding up the damage you take). Falling rocks, vines (environmental debuffs and cc are cool too - or even buffs and healing and whatever else)... the possibilities are endless.

Anyway, weather in particular.
- Area specific minievents would be interesting. Rain can slow regen and spawn more of some animated (or new animated - water or mud fluffs come to mind), while perhaps adding debuffs against others (for Bassken, which would fit best for rain I'd think, saws might get Rust of some kind). Winds could provide knockback in a direction, and maybe damage for sandstorms (or loss of accuracy or such). Lightning as a rare effect during rain (an animation and sudden health drop, with negative [armor loss, accuracy loss...] or positive effects [after all, this is zOMG, so getting hit with electricity might make you faster or something cool])...
- An overarching most-maps minievent would be really cool. Special graphics would have to be limited. I'd suggest darkness and sound effects for rumbling cloud formations. Add in lightning, Hail Fluffs or something (some kind of common spawn that would appear in different areas and add some trouble), maybe some knockback (wind) effects, some rain (debuff, maybe some buff) effects, and a reachable instance (a map [anyone can go to the same instance] or "large" instance [more than one crew worth of people can go there] could be optimal) to the top of the clouds (an instance that would pop up connected to the CL associated with the map, on any map the minievent popped up in - the players could go up and fight a boss up there).*

*What would be cool is if the boss could also be affected by anyone below or above the clouds. Those at the top would face the boss (I'd think The Eye of the Storm would be appropriate) at its weak point - reasonably low health, but normal boss resistance to cc or debuffs. Those in each map the storm was going through would face it with a lot more health, but be able to use crowd control and debuffs to some degree. The upper map/instance could move along through each map as the storm minievent moved across them (if that was implemented). When the boss was defeated, the clouds would vanish and those from the upper instance would fall into the instance they defeated it in (maybe with some substantial fall damage - just for the scene of tons of players falling from the sky, with some dazing from it for realism and challange).