I am working on a Druid build that takes 10 levels in a prestige class that does not advance their Animal Companion. Are there class variants that replace the Animal Companion without affecting their Wild Shaping in a negative way? Or should I not bother with these?
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The list of Alternate Class Features has several options for Druids who want to drop their animal companion.
Furthermore, there are several ACFs that modify Animal Companion instead of dropping it completely. It might be that you can gain something from them even without full progression.
Druidic Avenger (Unearthed Arcana) can trade animal companions, spontaneous casting, and a wild empathy penalty for Rage and Fast Movement. No effect on Wild Shape
Urban Companion (Cityscape Web Suppliment) lets you get something more like a Familiar. This still scales up somewhat with class levels, but it's got a higher intelligence and can talk to animals of its own kind at level 1. So it might still be useful to you. Again, no effect on Wild Shape.
It's not for 3.5, but Pathfinder solved this issue by making the animal companion optional with an easy-to-backport change. Instead of the regular Animal Companion class feature, they instead get one called Nature Bond which grants access to either an animal companion or a subset of cleric domains.
Pathfinder domains (unlike 3.5 ones) grant two decent abilities as well as a set of spells. Your GM could back-port this by either just granting access to a 3.5 domain (as per 3.5 cleric) or by using the full Pathfinder version of the domain. Likewise, your GM can choose to stop your domain progression if you stop taking druid levels or could let you keep advancing the domain. But even if your domain progression stops at 6th level, you'll still have a few extra low-level spell slots and a domain power, which will be more useful than a low-level animal companion.