I remember the feng shui and restaurant missions from Hong Kong.
Yeah, the idea for both of those missions (and others, like the convention or the movie party) are interesting. The execution though? You don't really do anything in either. For instance, in the fengshui mission, all you're doing is clicking on any spot that comes up on the screen and getting a message that you messed up the fengshui.
The corporate mission
Sheepherder, if I remember correctly, has an executive's office where you can examine their various personal effects to try to figure out their password, which you can type in with a parser. There are dialog based stealth situations where you need to sneak up on someone without them noticing, and if you don't choose carefully and use the right checks the whole thing falls apart. You have to carefully pick the right conversation options with the cleaning lady to talk past her.
Or the cybertroll mission he mentioned. There's a room that's inaccessible because of contamination, but you can use the parser at another computer to research what chemical you need to counter it (and you can research several other things as well). Because it's using a parser, you have to actually put some thought into it, not just mindlessly click. I only recall Hong Kong using the parser for interesting things once in the Shadows of Hong Kong mini-campaign.
You have to put some effort in, and if you get things wrong things get much more difficult. In Hong Kong, non-combat stuff is usually mindlessly clicking on skillchecks, and even if you decide to forego those it doesn't matter since the combat is so easy.
There was also a very tough mission where you are supposed to choose between two factions, but you can screw both of them over and you get to fight them both in front of a building. There are two of those in the series actually, but one of them is in a park and is also tough now that I think about it.
Yeah, that was one of the harder fights in Hong Kong, but there are only a few of them and you usually only get them by intentionally choosing a suboptimal path. Also, I can't think of any that are well designed. Hong Kong encounter design seems to be about how many trash mobs get thrown down to kamikaze you, with easier missions having fewer trash mobs kamikaze you and less easy missions having more kamikaze you (I've heard HBS continued this kind of encounter design on Battletech).
Dragonfall has a variety of encounters; sometimes you're facing more numerous weaker enemies, but sometimes you are facing a small number of strong ones (the mercenaries in the subway, or the basilisk during the medical facility run). The fight with Gaichu's former team should have been like that in Hong Kong, but it ended up just being a fight with a few forgettable trash mobs you kill in seconds.
Dragonfall also had missions where the difficulty was based on interesting design. The cybertroll mission given above, for example - you have an uber killing machine under your control, but you have to rush to take out enemy hackers ASAP while being shot at or it goes over to the enemy. Or the end of Blitz's mission, where you have to take out another team in a locked room. However, there are four turrets in the room, two controlled by your side and two controlled by the opposing side. At the same time, you're in cyberspace with Blitz where you could hack the other two turrets, but there's another hacker trying to do the same, and also attacking you. There are a lot of moving pieces that make for interesting choices - do you ignore the hacker and try to change the turrets? Ignore the turrets and try to take out the hacker? Mix the two? Should you try to make your real world characters hunker down in a corner until Blitz succeeds in the matrix, or have Blitz try to create a temporarily optimal situation in the real world and take out the other team as soon as possible? Confounding matters even more is that you're not doing the mission with your team, it's your main character plus an NPC that only shows up for this run.