Of course, this isn’t the only way to make a multi-class system, but I think these are generally sound design decisions if you want to make a multi-class system as seen in many RPGs (like FFT, Blue Dragon, Bravely Default, Wild Arms XF, etc).
1) Use slots to equip secondary abilities & passives into, thus requiring the player to make choices rather than just allow everything learned to be used at all times (encouraging extreme grinding for ultimate characters).
2) Provide enough free slots to allow creativity and prevent feeling trapped into 1 or 2 best abilities.
3) Make it so that classes give all of their currently learned abilities and passives for free while currently equipped.
4) Ensure that classes aren’t useless at base level, thus allowing for late-game experimentation & emergency switching if the player’s planned strategy fails.
5) Reveal limited previews of future abilities to be learned thus allowing for planning. However, don’t do total preview to prevent the player from becoming bored with the job system early on (maybe just the next ability to be learned is revealed).
6) Give all characters innate attributes that distinguish them from other characters, regardless of class. Examples: stat differences (major stat differences, not just mild variations), unique usable items & equipment, exclusive jobs & abilities, etc.
7) Avoid making the innate character attributes & abilities too powerful – you want them to make each character feel unique, rather than invalidate the rest of the class system.
8) Avoid truly broken combinations – primarily combinations that render the player essentially invincible or able to take infinite numbers of turns or win every battle with no risk of defeat.
9) “Sort of” broken combinations, on the other hand, are to be encouraged since they make the player feel powerful & clever for discovering them.
10) Design unique classes – not just the standard Warrior/Mage/Healer generic classes.
11) Don’t overwhelm the player. If you give the player too many options, too quickly, they’ll just pick a few favorites and ignore the rest.
12) If equipment is class-specific, save class equipment load-outs to avoid having to spend too much time re-equipping.
13) Have fun!