If you want a 0 IV in speed (for trick room) or a specific HP (it's easier to get 31 than 30), it can be really hard, too...Getting a decent shiny through chaining requires: Synchronize lead (50% chance of passing nature) and chaining over thresholds for more 31 IVs. After 30 chains iirc your pokemon will halve 4 perfect IVs, so unless you were going for a zero speed special attacker, you'll allways ideally want to bottlecap it.
Honestly, the riskiest thing from sosing is the nature not passing. Apart from hidden abilities, it's the only thing that can not be fixed.
But I agree, nature is usually the worse, especially if you need the synchronizer out at the time of the call (?). Most synchronizers aren't that nice to use during chaining, and leveling each of the useful ones is annoying.