Except that the Ptolemaic agema would not be a separate unit under a faction like the seleukids, they would become part of the Argyraspides.
@bobbin

Yes you are right, the elite troops for each faction would not be available for the others due to the fact that each faction has it's set elite corps of elite troops.

@Arjos

Thank you for the useful information, it helps a lot.

Two questions though:

In EB the Seleucids and Ptolemies have both Pezhetairoi and Kleruchoi available, and both are considered the mainline troops or "backbone" of the army. In my mod that I'm making I am not planning on giving two "mainline" phalangite units to a faction because the player would choose one over the other and the latter would be neglected and a waste almost so who should stay and who should be left out?

My assumption is that I do the same with what I did with the Levies. If your in macedon or greece, Pezhetairoi would be your recruitment option, but if you are in syria or egypt. you would have to recruit kleruchoi. (Assuming you are playing as Macedon, Seleucids, or Ptolemies)

Would that be logical?

In my mod I have the Greek Cities having three Phalangite units
Militia Phalangits
Phalangites
Armored Phalangites

Now would it be better to keep one phalangite unit and add in the Thorakitai and Iphicratean Phalanx? Or keep it as is?

thank you all for the help!