The Alchemist yes, it's pet is not central to it's features, but the Archivists pet is important to a bunch of features.I mostly like the base class, but some abilities such as spell storing item and extra attunement slots should come online much earlier and then scale as you level.
I really dislike that all subclasses have a pet/minion. The alchemist and archivist pets could be optional through infusions, the turrets could be spells and the battlesmith seems like it tries to fit two concepts within the same subclass.
Overall the base class could have its abilities rearranged and it would be fine. The problem is the theme of the subclasses, which is too Eberron-centric and forces you to have a minion.
But I agree that the Humunculus fits better as an infusion, and I'd even go so far as to say so does the Iron Defender (high level infusion).