I noticed this the most when playing a sword and shield fighter and was taking perks in the block tree.
Deflects Arrows: Your shield deflects arrows that hit it - Shouldn't this have been part of the combat system to begin with? It's physics really and I don't think it should be related to your skill with a shield.
Elemental Protection: Negates 50% incoming magic damage - Once again, putting a thick piece of steel between you and a fireball just makes sense that it would deflect some damage. Why do we need a perk to do this?
Block Runner: Run with a shield raised - In real life I'm pretty sure I could hold up a shield and run, how hard could it be? Feels pointless as a perk.
Bone Breaker: Maces ignore armor - This perk isn't as big of an offender, but I do feel that maces should have had at least some effect of armor piercing from the start to set it apart from the other weapons.
That is just a few of them. My point is that I feel like Bethesda took a step back to look at their game and said "ok, now let's pick and choose which features to strip out and turn into perks". If a perk isn't a stripped feature, then it's probably a simple damage % boost or some other kind of overpowered variable.
I find the entire perk system really disappointing. Just take a look at F3 or F:NV. Perks never felt like they were stripped features that I'm slowly unlocking. They were great for defining each of my characters and were like icing on the cake (the cake being the already robust combat system).
Another way to put it would be; The Fallout perk system was like adding cool cosmetic changes to my car that were fun. The Skyrim perk system is like putting back all the parts of the car that were striped out of it. It just feels like the entire process of leveling up is doing this and it's simply padding. Really, really disappointed.

I always have to keep my guard up, and can't risk letting it down.