Am i getting this wrong or it's quite odd and misleading?
There is any way to overwrite a mutation?

If not (from the manual it seems that you can't), it's misleading because you get a lot (really, A LOT) of inferior quality mutations, but if you use them you're a bit screwed, and if you don't you feel always like as you are waiting for something better.

Wouldn't have been better if you could overwrite them (and maybe even armor enanchements), or if there weren't "inferior" mutations but only rare good quality mutations?

Besides this (and some elements of interface, like inventory and vendor interface which are really unhandy) this is really a great game, i even enjoy the combat system which is quite challenging and realistic even at normal difficulty.

you cant change them (according to the manual)

and its horrible. why the hell would you waste a slot on a low quality one you can never take back.

its like doing something illegal. it stays with you forever and you regret it

I'm fine with the mutation being permanent (it is, after all, a mutation; there'd need to be some kind of 'revertant-agen' to change something back), but mutagens seem waaaay too common loot. Especially when they're labelled epic/rare and you get them all the time!

well im saying why the hell would anyone use a crappy one when they know there are better ones out there.

You sell them. They are a primary source of Orens.

Which is very odd. Who the hell has use for mutagens except witchers? Maybe Kalkstein.
If I was a merchant, I would not buy anything I could not make a profit off. That is equally screwed as the ability to sell scrolls that were stolen from Khaer Morhen in TW. I held onto them and just put them in storage, because hell, I can't go into the world to get back the witcher SECRETS only to make a quick buck from it!

The mutagens being common (and the usable slots uncommon) is exactly the reason why you should be able to overwrite them.

Not to mention the fact that "impregnation" doesn't affect already-placed mutagens.

Yea, the system is silly. If you're a newer player, you WILL slot mutagents and you WILL slot whatever you have.

So what now? I'm stuck with mediocre mutagents for the rest of the freaking game?

I fell in that trap too. What is the point of having crappy mutagens in the first place, while also not letting people have a lot of slots for them? Do I wait until the very end of the game for all the super rare ones, do they ever come?

I think they should have allowed you to put in better version of the ones you already slotted it, that would have made sense. A mutagen growing to something more. Lesser gets bumped by a greater etc. So you are still locked to a choice, its just allowed to get better JUST LIKE EVERYTHING ELSE YOU HAVE.

Sure, live and learn. In a second playthrough I will have learned to cope with there poor design choices. I love the game but it really has a lot of issues being user-friendly, asking the user to just cop-it and adjust isn't worthy of praise.

I like them being permanent even after falling for this trap! But it would be nice if we could mutate further maybe even adding some negative values? Like you use a mutegen to have more strength then you loose some brains etc.

Also cross effects of certain mutations would be nice not sure if it is in-game coz I couldn't play the last few days. For now I am collection them mutagens to sort out the powerful ones to not waste more slots ;)

That or simply allow greater mutagen of same type to overwrite a lesser one. Which is a more simple solution and thus easier to implement in shorter term.