I'm not aware of any way to set rally points. It might be nice but to be honest I've never really trained enough units that it's been an issue. The number of cities and number which are training troops in an average Legendary Heroes just isn't on the scale it can be in a large tank war in Civilization, for example.
With heroes, magic, summoned units, etc., it's not hard to complete a game having trained fewer than ten units. Zero units except Pioneers is perfectly feasible. There are other parts of the user interface which I'd like to see improved first.