For example, you could start the game as a "Warrior" class, but initially, straight from the beginning, use your bow instead of heavy armour and swordplay. You would be more talented at using heavy armour and blades -- they'd just come naturally to you -- but you could practice really really hard with your bow and get better at using it than you could use a sword. Of course, if you practiced the same amount of time with a sword, you'd be much further along than you are currently.
There is also the issue of entertainment. Most good RPGs I've played are level based. The skill based ones where you increase skill by using a specific talent usually leads to you needing to do a certain task over and over again. This is very realistic but it can and probably will be very boring which is why I don't really like this kind of method. A classless model like the Exile and Avernum games is much better. Rather than repeating a certain skill over and over you just gain exp through killing monsters, when you level up you are given a certain number of points which you use to increase stats/skills. This is unrealistic in that a player could get all the experiance through using swords then buy a lot of magic skills, but it's a lot less frustrating than having to poorly cast magic over and over again over a long period of time to slowly increase that skill. Since it is game you are working on and not a simulation your prime concern shouldn't be how real something is but how enjoyable it is for the player.
A fighter has a distinct advantage over a monk in that they have a larger selection of equipment they can use so thier power isn't completly determined by level whereas a monk is very restricted in equipment thus his power is mostly restricted by level. A well decked out fighter can easily have more immunities, resistances, and all around firepower than a monk.