Honestly, you can't because from the ground up the class system is unequal.
Some classes get a passive that scales indefinitely with a stat rather than with class level, e.g. Monk AC, Dark Blessing, Divine Grace, making it innately attractive to simply beeline for a class feat and forget about that class afterwards.
Some classes get a abilities that scale indefinitely with class level, e.g. Enchant Arrow, Epic Superior Weapon Focus, Sneak Attack, Caster Levels, making it innately attractive to invest heavily in that class compared to others that don't.
Some classes have very common counters to their main ability, e.g. Sneak Attack which is resisted by anything with Crit Imm, Sneak Imm, Uncanny Dodge, Defensive Awareness 2+ etc, while others have abilities that will always be useful, e.g. Epic Superior Weapon Focus, Divine Might.
Some classes get bonuses at very slow increments - compare Ranger FEs vs. Arcane Archer Enchant Arrow, Barbarian DR vs Dwarven Defender DR.
Some classes have abilities that are not just disadvantaged by being temporary, but also limited by game engine caps - Paladin buffs vs Epic Superior Weapon Focus, Barbarian Rage vs RDD Stats.
The skill system is innately broken - you can hoard skill points and have a level 2 Rogue/Level 38 Wizard be a better trapper and lockpick than a Rogue 40.
Some classes are incomplete - Rogues for example are limited in ways to set up Sneak Attacks by themselves and hampered by low AB.
The game also heavily revolves around instant win mechanics and stacking immunities to ignore instant win mechanics - HiPS Stealth vs. True Seeing, Instant Death vs Death Immunity/Crit Immunity (if Dev Crit)/Mantles (Implosion), Mind Spells vs Mind Spell Immunity, Time Stop vs Counterspell, Harm vs. Shadow Shield/Conceal/Negative Prot and so on.
Think hard about what you're going for - if you're doing a really RP-oriented server, just do a light touch approach and live and let live. Your dev time is better spent on things that improve quality of RP. If you're going for a more Action-oriented approach, one method is to adopt a light touch approach as well and compensate with skill-based content - see Magical Master's Siege of the Heavens for an example, where challenge is based more on not standing in bad stuff and doing the right thing at the right time than optimizing your stats. Alternatively, consider a ground-up redesign where every class follows the same rules, receives class features at the same interval, and preferably, does away with the instant win mechanic vs. immunity meta in favor of universal mechanics.