[Menarker]

Keep in mind that it only becomes helping hands for Fire types during Sunny Day and Water types during Rain Dance which means that either there are a bunch of pokemons of the same type on the field, slayer users, or the pokemons/brids using the moves are using the moves without gaining STAB. This means a lot of pokemons of the same type are being open to the same type of attacks such as an AOE element of that type. A boss using an AOE rock type attack against a bunch of fire types side by side for example. Also, the foe could attack with the same elements right back for helping hand benefits (unless it got dispelled before they got their turn).

Besides, AB could easily build a group that focuses on the weather conditions and use it against us. Maybe instead of us always ambushing the foes and getting the first strike, the evoliths will have precast a weather condition (they are like sentries) before we have arrived and thus the evolith's allies could try to take advantage of the benefits.
IE: When battle starts, some conditions are already preset as a result of foes tinkering with the battlefield. Maybe there are Stealth Rocks already placed. Spikes. Weather of different types being applied. That sort of stuff. AB could easily make things more balanced just by having the things that were our benefits now become the foe's benefits.

And I still don't know how you can possibly come up with a plausible way to effect weathers because they all operate differently. Hail doesn't have the same helping hand effect and neither does Sandstorm.

I think the best thing to do might be to just limit the number of turns that weather lasts in general. Unless the pokemons have an ability to improve the weather (like Abomasnow, Tyranitar, Groudon and Kyogure who can all summon their own respective weather), someone equipping an item that increases the length of the weather, or if someone like Matthias who might specialize in weather control gains buffs in some way like this, make it so weather only lasts 2 maybe 3 turns at most instead of the standard 5.

But I don't feel the weathers are unbalanced otherwise. AB just hasn't made them a huge focus in his battle plans just yet.