Last night, I EV trained Dialga and Palkia (Ubers, I know, but I like to be prepared for an Uber match, just in case). It's interesting how their defenses are opposite: Dialga has a base 120 defense stat vs 100 sp. defense, and Palkia has a base 120
special defense vs 100 defense (I never noticed...)
This morning, I started capturing the new in-game legendaries (the trios). First I caught the Regis, but I didn't worry about natures; I don't plan to use them competitively, and even if I did, I have ruby, sapphire, and emerald for that. Next, I caught Mesprit, not worrying about its nature. I did, however, want good natures for the legendary birds, which is a little harder to do, considering they roam the wild. Luckily, the first set I caught was good enough, with the exception of Articuno, which I never use anyway.
As soon as I have time to focus, I'll start breeding Eevees. I only have 1 female Eevee, which is on my Diamond version (actually, I believe it is a Glaceon). I haven't checked its IVs yet, but if they're bad, I'll just use one of the Dittos I have (one of them has max speed). My main goal is to have Vaporeon, Jolteon, and Espeon at my disposal, but I love all the forms, so eventually I plan to train a full set of Eeveelutions.
Lastly, I'm only 2 Pokemon short of being "version independent": Mewtwo and Latias. Unfortuately, I traded away the Mewtwo I had (bad nature) and restarted both Fire Red
and Leaf Green.

However, I think my Emerald game is past the Elite Four (choosing Latias) so that will be easier.