Well I think the perks will have descriptions of what they will do, and I don't think can really do a "crucial mistake" with them. The perks will have skill restrictions, so if you are using swords you can't take all the axe perks and why would you anyway?
No as I remember in Fallout 3 few perks had a downside, yes many who selected bloody mess got bored of it, you also had the law bringer and contract killer who excluded each other.
But except from this only downside was that you wasted a perk.
However you might find it useful later, take maces and a perk who ignores armor, it would be weak early in the game then enemies has weak armor and low skill, however it would be far more useful in level 50 dungeons against enemies in ebony and daeric. :toughninja:
I'm also pretty sure it's a console command for adding and removing perks, it was in Fallout 3 as I understand.