Good Afternoon. Zephyo here!
The whole idea behind multiclassing and taking a prestige class is to create a fun character with an concept that is better than the sum of it's parts. However, the system is very punishing for people who chose to specialize their character, and assumes that characters don't bother to keep practicing what they've already acquired
For example, with a Magus 6/ Rogue 4/ Arcane Trickster 10, the character caps his Arcane Pool at 3+ Int and can only enchant his weapon to +2, and his Trapfinding bonus caps at 2, and his Trap Sense is a paltry 1. These skills, essential to the core of their classes mechanisms, are entirely crippled. And to reference, a Magus 20 has an Arcane Pool of 10 + Int and can grant a +5 enhancement bonus, and a Rogue 20 maintains a Trapfinding bonus of +10 and a Trap Sense of +6. Clearly, the multiclass will never keep up; they just aren't designed to support the abilities they acquire.
Thus my idea, the Prestige Supplement Clause: Levels in a Prestige Class stack with the Classes that qualify the character for the Prestige to determine the effects of (Su) or (Ex) Class Abilities he or she already possesses. Spells per day remains unaffected. You cannot stack Prestige class levels.
Prestige Classes always have Requirements. The Arcane Trickster, for example, requires the character to be: nonlawful; possess Ranks in key skills; be able to cast any 2nd Level spell along with Mage Hand; and Sneak Attack with at least 2d6 die. A Magus 4/Rogue 3 can meet all of these requirements, so when the first level in Arcane Trickster is taken, the abilities this character has already learned will continue to grow as they are designed to do so.
So, the Magus 6/Rogue 4/Arcane Trickster 10 from before had his class abilities limited to levels 6 and 4, respectively. But now, for the purpose of his acquired class abilities, he is a Magus 16/Rogue 14:
|+| The Arcane Trickster's Arcane Pool is now a healthy 8 +Int Mod. He can expend a pool point to give his weapon a +4 Enhancement Bonus, or spend some of the bonus on weapon enchantments.
|+| His Trapfinding, on the other hand, is now a hearty +7 bonus, and his Trap Sense is a +4. Not full Rogue, but pretty classy all in all.
I feel that this Clause lets multiclassing characters keep pace with their fuller progression variants, as well as keeping Archetypes open and appealing to those looking to zest their characters further. And the way it is written, it works just as well for a character with two base classes as it does one. To conclude, it seems ridiculous that multiclass heroes stop practicing the skills they've already acquired once they've decided to attempt something new. Thanks for your time!