I believe the intent of the 1upt was to alleviate the burden of dealing with SOD's that could number upwards of 100 or more. Permitting 2 or 3 or 4 units per tile certainly accomplishes that goal without creating the headaches of moving units around, or of being unable to protect mounted units from attacks by spearmen. It was an over-reaction, one with good intent, but still an over-reaction.
First of all, spearmen should never be able to attack mounted units. I mean, really, how are persons equipped with 10 foot spears really going to be able to chase down men on horses?
This should be a game mechanic that spearmen can't even attack mounted units; defend, yes, attack, no.
Battles should be fought by cavalry on the sides, and infantry in the middle, with the winning cavalry being allowed to flank the lines. Prohibiting infantry units from attacking cavalry units would help this mechanic play out.
This way, mounted units would be able to move about and attack without impunity, all the infantry units could do is build a wall and entrench themselves. Now this, this would make the game believable and make it feel more authentic.
And yes, we should be able to stack naval units with embarked units as protection. That's so obvious.
The rule is too strict, and is hurting game performance.