1. The name "Greek Cities" while there were two leagues and have been melted in one by CA the main objection that i have is the separation of the Makedonians from the greek mainstay there is no need for me to exxaragate into analysis and evidence as every sane person knows that MAkedonia was the homelad of the migrating to the south greeks... So i would suggest the alteration of the name to the "Greek League".
No, I disagree. Do you know how the greek lost to the Romans? It was this separation from Macedonia and Epirus(which should be separate). The Greek Leagues had many wars with Macedonia so they got allied with the Romans. Did you really think those crappy Romans could muscle us down militarily? Well After Macedonia was almost destroyed and the greeks weakened the Romans smuthered the greeks slowly. Then they finished off Macedonia.

2. The whole Phalanx implementation is completely OUT of this world: Apart from the miserable fact that every backwaters nation in the game uses the disciplened formation its also not correctly implemented for both the classical and the Sarissa formations:
Not every nation uses it. I agree with you Germans shouldn't have it. Get R:TR 5.0 to have that fixed. The rest do deserve, in fact i think egypt should have the long pikes. Again R:TR.

As the classical formation should have used the spear attribute with 2 meters spears OVERHAND!!!
The intermediate Phillips Sarissa phalanx should use the short_pike attribute and underhand with large shields (ASPIS NOT hoplon=weapon!!)
The hypaspists have that short_pike you want. Most of them though had the long kind, let's face it.

The Successors PIKE sarissa phalanx should use the 6 meters pikes with BOTH hands underhand with small shields hanging from their arm.
The phlanax SHOULD have the option of CHARGE!!! It was used offencevly the pikemen were running (on straight direction) and CHARGING to batter the opposition so their formation will have a purpose and be actually DANGEROUS!!
Why not Alexander's as well? He had it. As for the two hand thing and the shield I agree with you, the game really failed in that respect. Hopefully they can fix it in the expansion.

As for the horse thing i don't know what could fix that. I certainly agree with you.