Kibou: I kind of assumed that it's obvious that a system that is flexible and adapts to the user is superior to one that only works in a very specific way.
I am for the user adapting to the system. I'm not exactly sure what you mean by the system adapting to the user. I mean, the devs can make sure that the game is fairly balanced regardless of your build, but asking for the system to be adaptive? Do you mean something like the game "detects" your build and changes some variables because of that - an example of which is enemy levelling seen in certain games. Choice and consequences is a different thing - the user still gets to choose. Lemme give a generic example, let's say you're good at stealth, you can still *choose* whether to pick the stealth approach, forceful approach, or diplomatic approach. It's just that you would have a higher chance to succeed at stealth approach. So this is not the system adapting to the user (i.e. the system automatically assigns stealth approach since your stealth is high) but the user adapting to the set rules of the system (the system has 3 options, the user chooses to invest in stealth and to tackle a quest via stealth).
Back to the topic of mutagens. I have never really relied on mutagens. I think it's one of those "perks" (much like abilities) which makes life slightly easier (or your build more overpowered) but not necessary for smooth progression in the game. Like someone said before me, this game does not encourage character optimization, at least in the conventional sense. Just look around: you don't have to grind to level up (main quest is the main source of experience), you don't have to farm for equipment (you can buy/craft slightly inferior equipment from vendors), low mutagen drops, the lack of item storage prior to 1.3 (to prevent hoarding of super equipment such as the Broom, the Shovel, and the legendary Pick as well as the 80 pieces of iron), the lack of the need to acquire "powerful artifacts" etc.
I mean, the game seems to eschew some of the more tedious part in character progression and inventory micromanagement so that the players can focus on the story, the details on the environment, and just getting used to the combat mechanics. You can be sufficiently well-equipped with vendor wares and if you are decent at the mechanics (have sufficient grasp on timing, dodging, and handling large groups), you don't really have to farm for mutagens or get the best equipment, nor do you have to fit the most powerful runes or most powerful mutagens in all the slots (although you can cut down enemies faster with those). Admittedly, the traditional RPG players in us would be tempted to max out our abilities, max out our equipment, in which case it's fine to hold out until you get the greater mutagens and do away with the "useless" lesser mutagens.
So what do I mean to say in this unnecessarily long essay? That being able to exchange/upgrade mutagens in skill slots is not necessary, If you need the instant boost to carry you over through the arguably more difficult initial part of the game, just plop in a few of those lesser mutagens. If you want to be the most powerfullest badass slayer of man and monsters alike, then hold out for the greater mutagens. If you had used some lesser mutagens earlier on, will you end up for worse in the later stages? No. Will you be less powerful than those who held out? Yes.
That is all.