If I had to choose between the two, I'd probably keep the animal companion in most cases - it's more reliably powerful.
Assuming the feat that extends shared spells range to 30ft is in effect, I can see the animal companion is a good choice for both a melee focused or caster focus build, while AC seems generally superior for casters compared with wildshape.
Wildshape
Con - Confusing ruleset (can't comment on Rich's houserules as the site is still down)
Con - Power levels depends wildly on book access, and DM interpretation of familiarity with more exotic forms (dinosaurs, sand tortoises, etc)
Con - Can be (partially) substituted with other druid spells (Shapechange at very late levels, SpC's Aspect of the Wolf, Primal Form, Wild Runner, etc.)
Pro/Con - You can easily sink all your feats into wildshape and be much more effective at it, or only take Natural Spell and it's still decent
Pro - Can have dump stats in Str & Dex and still be amazing in combat (this gets better in point buy)
Pro - Assume Supernatural Ability plus Aberrant Wildshape opens up tons of T1-level cheese (double actions, beholder eye rays, etc)
Minor Pro - As a druid player, it's really satisfying to turn into a velociraptor and rip something apart
Animal Companion
Con - Can be (partially) substituted with Wild Cohort feat, Leadership, Draconic Leadership, or Initiate of Nature feats
Con - DMs can be strict about communication, or animal "fears" of unknown phenomena, or its mobility (tight dungeons, fearful villagers), or limiting new companions after 24 hours (vestiges of 3.0 AC rules are commonplace at tables I've played with)
Pro - easy to make very strong
Pro - free action economy
Pro - can boost its levels with Natural Bond if you decide to prestige class
Minor Pro - lots of good roleplaying potential