How about this idea: equippable pokemon. The ability to attach certain pokemon to certain other pokemon for added affects or otherwise. Like a remoraid to a mantine to increase special attack, or equipping a baby kangaskhan (which is an alternate form in this hypothetical game) which will activate its parental instincts and raise its attack, and be required for the baby to mature. They could even retcon evolution methods such as slowpoke’s and magnemite’s with this. Sound interesting?

…hmm.

That does sound interesting.

So, we would be talking about filling an item slot with them, I presume?  Let’s see… there’s a very limited number of Pokémon that this would work with, which on the one hand means you don’t get to do much with it, but on the other gets to emphasise the special qualities of the ones who can work together like this.  I can imagine the extra programming work being something of a burden, but there’s some neat stuff you could do with it.  Obviously all such Pokémon would need to be immune to stealing and switching effects, in the same way as, for instance, Giratina’s Griseous Orb.  I’d have an ‘equipped’ Pokémon gain experience with its partner, and possibly have their effects scale based on level or other stats.

Your Remoraid, for example, could add 1/8 of its own special attack to Mantine’s while equipped (to be honest I think you could easily go to ¼ without making Mantine broken – we are spending his item slot here, after all – but let’s be conservative).  Vespiquen’s Attack Order, Defend Order and Heal Order could all be changed to require an equipped male Combee, and have their power increase when Combee reaches certain levels (say, Attack Order starts at 50, increasing to 70, 90, 110 as Combee hits levels 20, 40, 60; Heal Order gains the ability to heal status effects at some point; Defend Order starts out just boosting defence by 1 stage, picks up +1 special defence around level 30, then changes to +2 defence at 50, and +2 special defence at 70).  And now male Combee actually have a purpose in life!

You could also potentially do some really weird stuff that isn’t immediately obvious – equipping Foongus to Paras or Amoonguss to Parasect, maybe?  That could maybe alter Paras’ Effect Spore to add ¼ of Foongus’ level to the percentage change of inflicting sleep (currently 10%).  Or Rotom!  Rotom could possess Steel-types to give them all the weaknesses, resistances and immunities of a Ghost Pokémon (or, if you wanted to do maybe a more sinister take, give them something like a 50% special attack boost, something really absurd, in exchange for automatically Cursing them at the end of their second turn in battle).

Isn’t there a sword Pokémon in X and Y?  (No, don’t answer that; I’ll find out in my own time).  Seems like it’d be a natural candidate for something like this.

Evolution might be trickier.  Slowpoke to Slowbro is straightforward, but what about Slowpoke to Slowking?  If Slowpoke has Shellder in his item slot, how does the King’s Rock come into play?  I guess Magnemite would work by equipping one Magnemite to a second (producing a sort of Eviolite-like effect that increases all of your Magnemite’s stats by, say, 20%), and then equipping the second Magnemite to a third, which immediately prompts evolution (if you cancel, the second Magnemite drops back into your party – no nested Magnemites!).

In short – sounds like fun!