I can't imagine the secondary units being removed from pike units, unless perhaps the most basic of levies are left with no more than a knife for a secondary. The main argument against this being that they did actually have secondary weapons. While I agree they're too strong from the front vs missiles and too resistant to rear charges due to the mass bonus of the phalanx formation, most of this is hardcoded and a result of the engine, not the EB team. They've hinted though, and I'm looking forward to, very different phalanxes in EBII.
Phalanxes look a lot more realistic in rough terrain. While they're still tough, try charging a phalanx frontally in a forest where you have a significant slope advantage - highly armored troops can sometimes get into and break levy phalanxes and even pezhateroi without flanking support.
Edit: As Vartan pointed out below, phalanxes are also more reasonable using fair play standards (even if the AI doesn't follow them) by not switching direction without leaving combat & phalanx formation and reforming.
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