Yes there was a switch around between shinobi and ninja between STW and MTW. In the latter Assassins became the cheaper unit that can be upgraded fully and is available earliest. For spies you need the castle, they're more expensive to train and the last building in the brothel tech tree cannot be built for some unknown reason. It is definitely an "overfix", in that it makes spies much less worthwhile. The tech tree for spies/assassins in the VI campaign was better IMHO. On the whole though, I prefer how Shinobi/Ninja are in STW.
Edit: for those that don't like border forts, you should be able to stop the AI building them in the building choices file. This will probably mean a lot more AI shinobi and ninja running around though.
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