You're confusing the linearity of the list of location with the linearity of things you do in game. Let's take a look at the last Taipei mission creatively called Stop Omen Deng:
http://alphaprotocol.wikia.com/wiki/Sto ... rial_Rally
First, even though you're a super awesome spy who's like really awesome at collecting and buying intel, there is no way for you to figure out that Deng isn't trying to assassinate the president. Second, you do exactly the same sequence: reach gardens, exit gardens, enter the hall, chase Deng in a very linear maze-like construction area, reach the top, fight him, and either spare him or kill him.
Consequences of previous missions:
- Turning off the bugs gets you help from G22 for this mission (help I don't need; if anything these fuckers started several fights I didn't want them to and triggered the alarm; thanks a lot)
- Not telling Hong Shi's men about what he did gets you back-up for this mission (same comments)
- If you kept Heck happy (or Taipei is your first hub), he doesn't sell you out at the end of this mission (which affects a few dialogue lines)
Consequences in following missions:
If you kept Deng alive he will give you information later in the game (how does it affect the following missions? It doesn't. Should have killed the fucker.)