Hey, I was thinking about posting something among these lines as well.
After finding current missions more boring than usual, I spent some time thinking "How to make more interesting missions?". And to structure my thoughts on how the current state could be made better, first I had to define what the current state is. I concluded something like you did: the problem is not with missions themselves, it's with where those missions take place. The problem is with level structure.
I ended up with the following: non endless missions are constructed of at least three different rooms: spawn room, (at least one) objective room, extraction. Everything in between is just a collection of differently shaped corridors, since they don't offer any reason to exist but to generate more enemy spawn points. This way, the only thing that is capable of creating some form of drag (which results in engagement ) is hordes of enemies. And like you said, players can easily ignore the hordes and complete missions, thus reducing most missions to a race to extraction. But I asked myself: is this necessarily bad?
Picture this: after a long day, I return to my house and want to chill. I log in to Warframe, choose to do some quick rescue mission. When the mission starts, I realize there are five mini bases and archwing is required to travel through them. What is now done in a couple of minutes by doing a simple straightforward "go there, do that" could possibly take three, four times longer, depending on the mercy of RNG. And for what benefits would these missions be longer? It wouldn't necessarily make them more interesting: you would be applying that same straightforward approach in order to progress, but now you have to do that again, and again, and again. Is it better like this?
I like to think this may be one of Warframe's oldest problems. People used to rush missions with coptering, now with bullet jumps, in the future with something else. The way non endless missions are structured allows this and the only reason not to rush is because you don't want to.
Alternatively, I also agree with your feeling that missions could have more layers of complexity. Even if you don't rush, even if you try to find something interesting to do, most missions still end up being easy because they are conceptually simple. However, being simple is not the problem. The problem is offering nothing else besides that simple goal that could make you consider different approaches or different playstyles. Then, things start to get boring. What else could you play if not normal missions?
And thus came our open worlds. To allow a new, fresh experience of freedom. To release us from being rats in a maze. And after a while, well, you said it yourself: we don't care about most of it. Outside of said points of interest, there's basically nothing to do. Quite similar to our normal missions, isn't it? You spawn, go to your objective, complete said objective (usually by killing a lot of enemies), repeat, repeat, repeat, go to extraction/do something you can only do in open worlds. However, instead of having to go through several different rooms, you need to travel several kilometers. Then people got mad when they heard that Blink was going to get nerfed. It's not difficult to see why.
I think the problem with open worlds is that they were made to be vastly different from the places we normally have missions on and that's it. The intention was to have a different place and feeling, which we got, but it didn't quite solve problems we feel about normal tilesets.
I agree that there are several places in both open worlds which could benefit from having our familiar randomly generated tiles, and there are several normal tilesets which would benefit from having a larger/outdoors tile, but the simple mixture of them would not make everything better. At worst, you're just making missions longer since you have to travel more.
Picture this: a normal tileset with a large, free roam-ish tile. It's an Exterminate mission. There are 3 enemies left. You enter trough door A. You have doors B, C, D and E to go through, all separated by 200 m. It's a small scale open world: scattered interest points, just travel fast.
Let's separate them back. Indoors are indoors, like what we have now. For the longest time, I thought that having secondary objectives would be a great solution to how simple most missions are. "Let's have a Capture turn into an Exterminate", I thought. A lot of people, myself included, didn't quite like the result. Others have their reasons, but my reasons are: it didn't really change anything did it? You were doing a straightforward approach 1, then you were forced to change to straightforward approach 2.
Ok, so secondary missions are not good if they are forced. So let's have them being optional. Now you are playing a Mob Def. While moving to another room, you pass by a spy vault. Ordis says that if you wish to, you can hack it. You decide to hack it, carefully moving as to not trigger any alarms aaaaand it's done. You proceed to continue mob def as normal. Was it worth it? By the perspective of both devs and players?
So, secondary missions, even if optional, even if within a mix of indoors/ outdoors, are not a really meaningful solution. At this point I ran out of concrete ideas.
Now I don't know if what I'm going to say makes sense, but the only thing I believe can make gameplay more interesting is: to make us less capable of doing missions by ourselves. It's not about nerfing or power creep, it's about restrictions, or currently the lack of, that are imposed to us during our gameplay.
Explanation: the other day, for reasons, I was comparing vehicle gameplay in Warframe to two other games I have played: 1) Halo (the first one), and 2) Borderlands 2. Generally speaking, vehicle gameplay isn't common in them, but when you have the chance to drive one, it is awesome. You get a high degree of mobility + some awesome weapons, but for a short time. There's always a limit to how much you can progress, usually in the shape of a narrow passage. Then you're forced to abandon the vehicle and move along.
What makes using vehicles awesome is that you momentarily lose the "restriction" of being a squishy, weak walking pleb. You suddenly get much faster, more resistant, and stronger.
What I'm trying to say is: in Warframe, you're always in a vehicle. You are a naturally high mobile killing machine with various degrees of squishiness, from "paper thin" to "immortal". The only narrow passage used to be operator gameplay, and how narrow/ restricting is it? Invulnerability while being invisible, ability to quickly dash through considerably long distances, ability to slow, generate energy and crowd control, possibly paired with Magus Lockdown and/ or other healing arcanes... it's not restricting, it's even enhancing gameplay! But I'm not here requesting to remove this or that. I spent my time upgrading/ ranking up, it's good that operators can be useful.
Back to the point: this means that, after playing for a (long?) while, slowly upgrading, it won't matter how missions are structured, you'll eventually be able to not care about it. Either via warframe itself, or via operator enhanced warframe. This results in "restrictionless moments" never happening - gameplay ends up getting stale.
"Well, they have too much power and are trivializing missions, let's take them away". Then DE created nullifiers, and people got mad, because it took away their abilities? I think it's also because it disregarded their time and effort upgrading stuff. Upgrading is what drives people to play. No one farms for Blind Rage to waste energy in nullifier fields. No one pursues more power to lose it.
So, restrictions cannot come in a way that disregards our upgrades. Without upgrades (mods, arcanes), we are just warframe + guns and operator. To not exclude new players, we are just warframe + guns. This already means a lot. Making enemies sleep, staying invisible, creating shields... No enemy could be prepared against all kinds of abilities we have. Therefore, restrictions should not be applied by enemies.
So who should apply restrictions, if not enemies? This is where I wrap everything up: the tiles should. By creating specifically structured tiles, you could integrate optional goals/ more layers of complexity into your main mission. In one single mission, you would be presented with the option to go straight to the main objective, or try to achieve secondary goals. The results of sucessfully completing secondary goals could be harvested within the mission itself, by unlocking a different area within that tileset (which could even be in a previoulsy locked portion of an outdoor tile), or by receiving pointers to another mission, in another undiscovered/ unexpected place, where you can possibly find another different optional secondary mission. And you could stop this chain any time. It sounds weird to me today: you could choose to not play more.
The kinda good thing in this scenario is that people who want to go fast will still go fast, but people who want to find interesting things to do would potentially always also have something.
The bad thing about this is that we'd need quite a large production of new tiles for every tileset. These new tiles would take advantage of each tileset's theme in order to generate a secondary mission that, when played in that tileset, it would be different from when played in another tileset.
My verdict is: I surely hope something changes, and changes to something better. But honestly, that will take literal years. So probably nothing in the scale we want will happen. Maybe something in a smaller scale, but I don't think that would be enough. Sorry for long post and formatting, wrote on phone.