Hello BB,
1. STW was the tw game with the clearest RPS gameplay. In MTW also spears go after cavs, however they are defending and low morale units and so unfit really for chasing knights and other overpowered mounted horrors around. In STW spears are really a very decent backbone unit for all armies and all weathers, and - as advertised - effective anticavalry.
2. be aware that in the STW engine you cannot disengage troops once engaged, unlike in MTW. This strengthens the RPS as it makes match ups really an important gameplay part. As you noticed fleeing units also keep partially fighting, especially if you chase with units that can do badly against them, say chase yarisam with horse archers or warrior monks with yari ashigaru; expect casualties in such cases.
However as i mentioned in the past, be sure to patch your game to v1.12 - as version 1.0 (unpatched original) suffers from the infinite charge rout bug ie units that flee get and infinite frontal charge bonus. This effectively makes encirclements impossible as fleeing units instead of being massacred in enclaves they brake through while inflicting very heavy casualties to the units that stand in their retreat route. If you haven't done this you may lose battles and Daimyos that you should have won.
3. The upgraded towers do catch them though - although they are a tad too expensive - prefer Shinobis instead.
4. In fact historically during Sengoku Jidai, kenjutsu and all the arts of the bugei (martial arts), underwent profound transformation and development and by the middle of the period a number of outstanding masters that had fought dozens of battles and duels throughout the country were given patronship by the Tokugawa's and other winning Daimyo's. Such a case was Kamiizumi Nobutsuna (who by the way appears in the game as an Uesugi hero/general), that tought the later official intrsuctors of the Shogunate, the Yagyu family his yagyu kage (shadow) ryu (swordmanship school). The family moved to Edo after being invited personally by Ieyasu in the Edo period (from their original fiefs in Yamato) where they kept instructing all the Shoguns of the Tokugawa dynasty and producing such legendary figures like Yagyu Jubei.
The game represestation of the phenomenon is quite accurate; such masters made a name for themselves in inter-clan Sengoku warfare, Kamiizumi Nobutsuna in particular headed a legendary unit of 13 spears in a small uesugi-allied border town in Kozuke against the assaults of the takeda that heavily outnumbered the garisson. Shingen that was directing the assault personally asked Nobutsuna to join the Takeda, but he, politely, refused and continued on his path towards perfection of the kage ryu that he was developing with his two assistants.
PS Shingen did left his mark on the man though by sligtly changing his name; the Nobu of Nobutsuna comes from the nobu of Harunobu, Shingen's original name prior to becoming a buddhist monk.
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