Chosen templates seem to be fixed as LA +4 (at least, the Chosen of Mystra and Bane are). Employing them has several consequences:
1. Chosen abilities should be extremely powerful to reflect the high level adjustment. We're talking at least Half-Fiend or Half-Celestial powerful here (although these templates are very weak for +4). That includes hefty abilitiy score increases.
Chosen of Mystra gain +10 Con for some reason. Chosen of Malar might gain +10 Str instead, or +4 Str, +4 Dex, +4 Con, or some such. Also, spell-like abilities should include some fairly high-level spells (Animal Growth, Animal Shapes, Bite of the Were-X, or Shapechange for Chosen of Malar?), as well as some good at-will SLAs (maybe Pass Without Trace, Speak With Animals, Dominate Animal, Magic Fang, Summon Nature's Ally IV).
One or more really quasi-unique flavor abilities should also be part of the package. How about a Rage ability that also transforms you à la Wildshape?
2. High level adjustments are really hard to make balanced in most games. This is especially true for caster PCs, who will almost always lose out on LA, as it puts higher-level spells out of reach. Only very rarely will the template's abilities make up for that kind of loss. But noncasters will suffer, too, since they lose hit dice complete with BAB, saves progression, skills, feats... what seems to be a powerful template at first glance is almost always unplayable or at least a pain once LA goes higher than +2.
3. Chosen are supposed to be really, really unique. There's usually only one Chosen of any given deity around, AFAIK (Mystra making an exception on the grounds of being just that awesome, obviously). So the PC who becomes a Chosen will naturally become the focus of his deity's religion in the whole world. Even a god such as Malar, who doesn't seem to lend himself to worship readily (what with the bloody hunter of the wilds stuff), will have tens of thousands, maybe millions of followers. The Chosen PC will become the object of worship, sectarian struggles, and theological dispute, as well as the target of envy on an epic-level scale. And we all know how a wolfpack solves such issues.
These are some points that should be very, very well considered before you bring Chosen into the game as an option for PCs.