Interesting thought, and I can see where you're coming from.
But how do you resolve that?
A penalty is given for any offence that would result in a direct free kick had it occurred outside the penalty area - and like direct free kicks the way the game restarts doesn't vary dependent on the severity of the offence; that's dealt with by way of the sanction against the player involved (no card, yellow card, red card with one game ban, red card with three game ban, red card and additional sanction [eg Paolo Di Canio when he shoved the ref])
So its inevitable that there will be disparities - eg a two-footed leg-breaker a centimetre outside the box is a free kick, but a tiny clip of the ankle on the line is a penalty.
What are you suggesting? Splitting the direct free kick offences into two subsets where only the "severe" group results in a penalty? Something else?
Not sure I've spitballed this before, but penalties are now very overpowered. The goalkeeper is at a significant disadvantage and about 80% result in a goal. This is worse now that penalties are given for more innocuous offences in the VAR era, and more penalties are being awarded.
"A penalty is a special direct free kick given for offences inside the box" is not satisfactory and hasn't been for some time.
I would recommend a two tier direct free kick offence sanction inside the box. Handballs which are unintentional and innocuous and not denying an obvious goal should be penalised with a direct free kick inside the penalty area 12 yards from goal, with defending players allowed to place themselves 10 yards from the ball as with any other direct free kick. The placing of the kick should follow the same rules as an indirect free kick offence committed inside the six yard box, so, not necessarily on the penalty spot but in different positions around the penalty area, all 12 yards from goal. You'd still get a fair few goals from this - remember it's a direct free kick - but not 80%.
Everything else requiring physical contact with an opponent (tripping, kicking, etc) is still a penalty, as well as cynical and deliberate handballs like a handball on the line. However, penalties should be modified. The goalkeeper should be allowed to move off their line
as soon as the whistle is blown. This would make for more interesting and less guaranteed penalties. Will you do a one-stepper and take advantage of the wide angle before the goalkeeper gets a yard off their line, or will you take a few steps and read the goalkeeper's advance, all the time he's narrowing the angle? This would bring the scoring rate down from what it is at the moment and increase the interest in penalties, which, in my view, are very boring and too easy a goalscoring opportunity for a professional footballer.