However, this system has some complicating factors. First off, every character in the game has a specialty they are naturally good at. For example, some characters gain more bonus Melee experience points when they level up, while others get more Dodge experience point. Furthermore, characters gain special skills at different experience values. For instance, Royd gains his fist Melee special skill when he has 700 points in his melee skill, while Natalie requires 1000 points. On top of that, some characters have fewer skill slots that other characters, and some characters can't even learn specific skills. Yeehin, for example, is a Short specialist, like Natalie. However, while Natalie can learn all three Short skills, Yeehin can only learn one specific one. As a result, different characters have radically different customization options and potential.
The real problem is that all of this information is completely hidden from the player. While it is possible to infer from character's starting stats what they are generally good at, there is no way of guessing what skills that can learn and when. So, the player is forced to either start specializing characters blindly, or consult a strategy guide. While there is a customization system, it is so opaque to the player that it denies the ability to plan things out or make meaningful decisions. As a result, the system is not very fun to tinker with.
Unfortunately, a lot more games than just Front Mission have this problem, including several relatively recent games. Tales of Symphonia requires each character to choose a specialization between Power and Technical, without giving the player any idea what exact powers either specialty grants. Final Fantasy XII forces the player to explore the License board without any foreknowledge of what abilities there are and where they are located on the board. Most Fire Emblem games don't tell the player which characters can build support other, how long it takes to build support levels, nor what the benefits are until the support is already in effect. Even Final Fantasy Tactics, which otherwise has excellent transparency, still doesn't tell the player how to unlock classes until they are already unlocked for at least one character.
In order to make informed decisions about how to progress a character it is necessary to know ahead of time what the character will be gaining, and what they will be giving up. A good example of a game with good character customization is Xenosaga Ep. 3. In that game, every one of the characters has two skill paths that represent very different customization focuses for each character. Thankfully, every ability on both paths are available the player's viewing from the get-go (with the exception of ultimate abilities at the very end of the path). So, the player can make a though out decision about how each character will specialize and how to balance the team out with these decisions.