Well, one way to overcome that would be to make Toxic and regular Poison different. Toxic gets the crawling damage, whereas regular poison gets the stat drop.One thing I have been quietly wishing for would be a status that either halves Sp Atk or knocks defenses down one stage. The obvious contender would be poison... but that leaves the question about Toxic being so damn common that Sp Atkers would be Fubard.
Now this sounds like Digimon. It's been a while since I played Digimon World 3 and 4, but I believe those let you put items on your Digimon to make them stronger (though it may have just been 4, and only the weapon). However, I know the DS games ("Digimon Story") have a weapon, armor, and accessory slot for each Digimon.On the topic of unusual and wild ideas - how about armour? Wearing armour changes a Pokemon's secondary type to that of the armour (or adds the secondary type to a pure type). Perhaps only on the defense.
Steel armour might end up virtually everywhere mind; the type's so good defensively it may have to be omitted from the armour list (but then that wouldn't make much sense anyway). Certainly those Pokemon with a 4x weakness, especially to rock, would appreciate being able to lose it.
I'm not sure the theme is where Game Freak would want to go - but various sorts of armour have appeared in the anime: Mewtwo, and the war scenes in the opening of the Lucario movie spring to mind.
Honestly, the biggest changes that are likely to happen are things hinted at in HGSS. That is, true 3D worlds and sprites (as opposed to faux-2D), alternate outfits (Team Rocket, Jersey), possibly "alternate" Pokemon like Notch-Eared Pichu, customization (Safari Zone, possibly expanded to further areas), and things of that nature.