if im a mind flayer, a creature class, i get these racial type powers, maybe i get psionics, maybe i can levitate,
i get a physical form that gives me various resistances,
but then d&d comes in and tries to pin a class on this,
there is no class for this, its a monster class, the mind-flayer did not go through training school,
Class and race are two different things. Mindflayers can have class levels, especially if they're player characters. A mindflayer with a few monk levels is a mindflayer who has trained specifically to be more effective in melee, and better at incapacitating their foes for that tasty brain-nomming (stunning strike, anyone?). The mindflayer with class levels is intrinsically more powerful and dangerous than the mindflayer without class levels. Monsters do, in fact, play by the same rules, more or less; they generally don't have formal class levels, however, and are
universally much more scary and dangerous when they do.
The others have covered most of the points in the original post, and I don't need to go over them too much, but as to the question of needing to be exceptional... It's because you do; by definition, you need to be someone who is, or has the capacity to be, exceptional in some way, compared to most others. Choosing a class is illustrating the way in which you are exceptional compared to most others. It is a premise that you are above average; the class system is just asking you how you are.
IIf you want to take your first level in commoner, and get nothing but a hit die increase, a Dm would probably let you; you'd have no abilities, no skills, and no proficiencies, and if you wanted to gain them, you'd need to train them, and it would take time; time that you'd spend learning the basic proficiency and function of things to be able to use them at a reasonable competency, while others are improving their existing skills and growing stronger. Picking a starting class is the assumption that you've spent a certain amount of time off-camera gaining the basics of a few skills prior to this point in your life. You can choose not to have any starting kit at all, but you are only nerfing yourself if you do so.
Some small extra notes:
The problem i have with classes, is that once i choose a class, then it takes away the option for all the other classes
No, it doesn't. There we go. Now that that's solved - if that was 'the problem' you had, I take it you have no problem with it now, then? Great.
every character essentially wants to be good at everything. lets face it that's a fact.
No, it's not, and no they don't. It might be true for you, and for every character you personally create (and boy does that sound boring, but you do you), but you are not everyone. I have to disagree, just very mildly on one small detail, with PrivateRacoon here - Whether it's factual or not can't really be discussed in an intelligible way; it's straight up factually untrue. Not every character wants to be good at everything.