I would prefer the perk every three levels, also would like the perks to be more character defining as a trade off.
The reason I like this method, is basic economics of supply and demand. Having an abundance of perks devalues the worth of the perks.
The reason I did not like a perk every level, made them worth a similar value of skill points, easier to balance, but depreciated the value of perks to the point where they were akin to spending skill points you gain when leveling.
While perk stacking makes some nice combos, individual perks feel, 'meh', while in prior games 'sniper' and 'slayer' were gems. I like the feeling of gems, probably just nostalgia, but I miss it.
In my humble opinion.
Side note: The progression of my character in FO3 felt less like becoming my personal avatar, and more into the ubermench, I went through the motions, but my character died around level twelve. I also voted no snow globes and less skill points.