That siege-tower bug hits me very frequently. It's annoying. So very annoying. I end up using sap points and ladders if I can, or just don't assault walls.
As for the pursuit problems, what happens quite a lot (and more often in EB than in vanilla) is that a fleeing unit will get spread out, while the pursuing unit sticks together in formation. Then, when some routing soldiers are behind your pursuers and some in front the pathfinding will -think- your unit is in the middle of the enemy formation and your horsemen will stop going at full speed, instead keeping pace with the routers. Nobody gets killed.
This is very annoying, but it can be fixed with micro-managing: order the pursuing unit to run ahead of the routers, and when enough are contacting them/in between them, order to attack again. It's not a perfect solution but it helps.
Some of those other things sound just plain weird though. Some must have been bugs. Were those skirmishers standing on a massive wooded hill and your archers all the way at the bottom? A good trick for that is to just charge up the hill; the skirmishers will obediently skirmish away from your archers, so then when -you- have the high ground you can shoot and massacre them all in a few volleys.
In my Baktria campaign, by the way, the Parthians seized every Seleucid settlement up to Susa. They expanded faster than I did! I ended up attacking the AS just so I'd have some room left to expand without being squished by a giant Parthian empire at some point in the future. (My armies are now seizing Persia, the Parthians have everything north of there and are conquering the Caucasus now.) Goes to show it all comes down to the luck of the draw. In my Roman campaign it was the Armenians who conquered half the east.
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