It's a common complaint that junctioning makes all the characters too similar. However, by carefully selecting spells, abilities and GFs, you can totally customise each character into a specific role - for example, giving the Treatment and Revive abilities to someone with a lot of white magic gives you a perfect White Mage. Combat-oriented abilities, along with junctioning that enhances strength and defence, creates a Knight or warrior. And so on...
If you're really bored, it can be kinda interesting to give characters abilties that are completely different to their default skills - for example, making Selphie the indestructible beserker who can slaughter millions of foes with her weapons, or turning Squall into a non-combative healer.