Actually, while people keep talking about flexible "systems" this is actually a world definition thing.
Wizards cannot wear armor and only clerics can heal and rogues dont learn greatswords often is a small set of world defining aspects. They show the players how things work in the world. Your players are naturally falling back on the "fantasy worlds" they have the most experience with and its probably for a very simple reason.
"you do not seem to have defined your game world and its limits for them. The entire notion of "Only limitations are the ones you want " is practically anti-defining.
For example... if they want to play a toddler "normal human" who is as smart of the worlds smartest sage and has strength of 8 men, would you go sure? if they wanted to play a "normal human" who had six arms and a tail, would that be OK? Or are you going to stop and say "well that doesn't make sense?"
At the point that you stop them and say "that doesn't make sense?" you have just admitted "well there are some limitations... i just haven't told you about them."
Can your player choose a strength based skill for his magic skill roll? This way he can be a fighter mage and not have to fret with watsing points boosting int or ego.
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It boils down to something very simple... if you, the gm, had given your players a guide to "how things work in this fantasy world" they would know these things and try to play within your world as it makes sense and is explained. lacking a world definition, lacking a sense of things, and lacking any instructions as to what should be expected as normal... people are going to fill in the blanks with what is comfortable.
Should they expect normal squirrels to rush at them wielding two handed swords? Should this be seen in your world as just another hazard for those who do not drop adequate nutly offerings to the squirrel god?
Points (equal points or even very precisely calculated points) do not make balance happen in play. Instead, balance in play is what shows the points and costs were appropriate.
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