First - I'd love to be able to see IVs and EVs in-game. That'd make life a whole lot easier.
I've toyed with the notion of leaving the natures as they are, but decreasing the effect - maybe instead of +/- 10%, make them all +/- 5% or something like that. As it stands, I think nature has a bit too much of an impact. I'm not sure, but I don't think that'd have any lasting effect on the competitive metagame, since everything would change - sweepers would have 5% less attack, but walls would have 5% less defense, so it'd even out. And it would make it less punishing to use different natures in-game, which would make it more feasible to use natures that just seem appropriate aesthetically, instead of just Adamant or Jolly physical sweepers and Modest or Timid special sweepers and so on. It'd also make mixed stats and split EVs more viable.
IVs are fine as they are, IMO.
EVs are a bit strange - it doesn't really make sense to gain a greater ability for something solely because of the opponent's ability at it - but I don't know if they could be done better. They could be tied to what the pokemon does - using special attacks gains special attack EVs for instance - and that would make more sense in a way, but that runs into a whole bunch of problems that I won't go into here, so I guess the current system is about the best, odd though it is.
I'd love to see happiness have more of an effect, in part because that'd reward people who are loyal to their pokemon (which has been a fundamental part of the underlying message of the games all along, though only expressed in a handful of evolutions and the base power of Return), and in part, honestly, because there are some players who already rage at the apparently intolerable burden of happiness evolutions, and it'd amuse me to see them rage that much more because they have to actually spend time with a pokemon before it reaches its peak of power.
That last - having happiness have an effect on stats - is one I wouldn't be surprised to see, especially, as noted, with the hint they already dropped. It'll be interesting if they do.