The only thing I can really complain about with mods is that modded perks tend to be either overpowered, far too specific to be worth the pay-off, or work by adding skill points. Skill points are the big thing for me, since if you're focusing on a skill enough to want a perk, you'll max it in short order and probably it's relevant Special stat, too, and everyone gets to 100 skill sooner or later, anyway, especially with Broken Steel. I much prefer perks which add derived stats like damage or crit chance, though it's easy enough to tweak things, I suppose.
To try and make this thread slightly productive and not just a huge rant thread, why don't we link to mods which avoid the things we hate so much? Obviously, this isn't going to help the most general gripes(There are plenty of mods which aren't porm and/or throw realism to wind), but some concerns are more niche:
http://www.fallout3nexus.com/downloads/file.php?id=1198 and http://www.fallout3nexus.com/downloads/file.php?id=1176 both avoid the skill-point perk problem superbly by giving Unarmed Damage rather than(or in MAT's case , as well as) Unarmed Skill.
So, instead of increasing Strength, boost Melee Damage and Carry Weight. Not Perception, ranged weapon accuracy. Not Endurance, HP and Unarmed Damage. Not Charisma, not ever. Luck is crit chance obviously, just as Agility is AP. For weapon skills, boost damage or crit chance with those weapons instead, or make it boost only weapons of a certain type, like pistols only, rifles only, only knives when backstabbing(http://www.fallout3nexus.com/downloads/file.php?id=7636). The other skills, like Science or Repair, are obviously a bit more difficult to find viable alternatives for, but it's better than being useless.