Speed (or framerate at least) should not be significantly affected. All of the new units have full sets of LOD models and sprites.

Changing the movement rate back to vanilla is easy, but changing the morale and kill-rate back is a little more complicated. To change the movement rates you can either replace or edit the file for movement modifiers (unfortunately I can't remember the name, I can tell you when I get back, but it is in the data directory and the name is something obvious like data/desc_terrain_movement_modifiers.txt). To change morale and killrate you need to edit data/export_descr_units.txt.

I have only seen militia hoptites do well against Spartans in the town square. Not much that can be done about that - they get unbreakeable morale, and the phalanx formation itself makes them effective aganist anything.

Jumping horses can be fixed, although I haven't looked into doing it myself. I don't think I will include as default just because phalanx units are already very effective - but I might include it as an "extra".