Pathfinder has several placeholders for class customization within the existing framework. Let's work through them:
Feats & Traits
Many races & classes gain access to specific Traits and specific Feats. In fact, in the Golarion world, humans from different regions have specific Traits and Feats.
Adding a set of specific Feats / Traits for each guild seems entirely reasonable.
The default "favored class" bonus is +1 skill point or +1 HP / level. However, several races have special variants on Favored Class. For example Human Sorcerers can get extra spells instead of HP.
Providing such tweaks for guild members should be very reasonable. For example:
- Selesnya Druid: Add +1/2 level to the druid's caster level for summon spells. (go tokens)
- Dimir Wizard: Add +1/2 level to your caster level on Illusion and Necromancy spells.
- Boros Fighter: Add +1/2 damage on charge attacks (i.e.: +2 dmg at level 4)
- Rakdos Barbarian: +1 rage rounds / day
Archetypes, Domains & Bloodlines
Pathfinder has lots of "twists" on common classes wrapped up via Archetypes. The premise here is that you trade off certain class abilities for other class abilities.
For example the Thug archetype loses "trap sense" but gains "brutal beating".
So a Dimir Rogue might gain Passwall 1x day instead of Evasion, give them an incorporeal attack as a rogue talent, something that bypasses DR for a certain number of rounds. This would echo the "unblockable" stuff from MTG.
Most classes have a tremendous number of Archetypes. Making a "Rakdos Rogue" or a "Selesnya Paladin" Archetype is totally reasonable from a balance perspective.
For Clerics, Pathfinder has created Domains. Customizing a Domain for a given Guild would give each guilds Clerics a distinct feel without breaking the world. And it would fit with the premise that Rakdos cleric would be completely different from Simic cleric.
For Sorcerers, if you allow them, you can force a specific Guild Bloodline. Again, this would make Sorcerers distinct between guilds without really killing them.
Prestige Classes are a really big flex space. As written in Pathfinder they don't see a lot of use as they tend to be very specific and often sacrifice flexibility.
However, it's quite possible for you to develop some Guild-specific Prestige classes that maintain most of the normal level progression with reasonable class trade-offs.
So you could develop a Simic Prestige class that allows a user to continue to progress their Caster Level, but also gives them some abilities to grant conditional buffs to their party. (think +1/+1 counters)
What to choose?
Based on your criteria, Archetypes/Domains achieves your goal.
It is (1) flavorful, (2) optional, (3) rewarding guild behavior, (4) allows for different classes within a guild, (5) balanced (balanceable), (6) can level up over time.
Please note that Archetypes can be a lot of work. If you do 3 archetypes / guild * 10 guilds that's 30 archetypes! That stated, anything you do times 10 is going to be a lot of work. I mean 3 custom feats + 3 custom traits + 1 favored class bonus = 70 things you needs to create.
So lots of work, though, it could also be lots of fun if that's your cup of tea :)