Anyone else find this annoying, either that or im just not doing something right. I wanna be able to pick my grenade, my weapon, and perks, but its just confusing. 

Picking a weapon is easy obviously, but the subweapons and grenades are attacked to the gun. why can't i just select them?

and the perks? Well they are easy enough, just get them with the clothes. But once again, the clothes are random so, if you need something, you might need to wait a long time for a specific set of clothing just to get the perk, and the subperks are just random as well.

I really love this game, its addicting as hell, but some of nintendo's choices make no damn sense and make the game more confusing thansimple.

Because that would make certain sets very OP.

When it comes to sub weapons, I think having them preset is fine, mainly cause it prevents OP sets, like Bubble + Roller.

As for the perks, I agree that it's pretty annoying, and I hate how you have to be level 20 and spend a lot of money just to reroll and upgrade cosmetics.

The game hasn't been out for a week and lots of people are already level 20. You seem to level up pretty quickly. What seems like "a lot of money" after a mere 3 days of acquiring currency might not feel so steep after 3 weeks. Nintendo will also distribute free super sea snails through the Splatfests.

The last thing I want is a bunch of people spamming OP sets or whatever.

Balancing

The preset subs and perks were likely set to act as a sort of balance between sets. There could have been situations where people find the best combinations and stick with them. While this is limiting on what you can do customizing wise, perhaps it makes it better in the sense of having variety and pros/cons to a set. Same with clothes, though being to have your fav clothes with your fav perks would have been great.

Nintendo didn't wanna put the effort into balancing all the perks and sub weapons on their own so they balanced the game in the worst way possible, by restricting the player.

Having preset combinations helps with balancing so I'm not too bothered by this

They give you at least 2 different combinations for each weapon. It's the best they can do at the moment and they might change some stuff in the future. I think everything is actually perfect in terms of classes. No complaints on that front.