HeXen's puzzles aren't really that complicated, it's mostly the size of the puzzles, along with the theatrical presentation of the levels and puzzles that make the game so beautiful.
I'll break this down a bit, because I really really really REALLY want HeXen to live on, and I think Oblige is a perfect tool to breathe new life into it. If I could click a button and have an episode of HeXen to play I'll be able to die happy
Anyways, HeXen levels are different from Doom in that you can traverse between levels within an episode at any time through a system of portals. There's typically a "crossroads" kind of level with a whole bunch of portals that can take you to any level within the episode. However, there are some portals in certain levels that take you to other levels, bypassing that "crossroads" level. Sorry if that's confusing, it's kind of hard to word properly.
There are some puzzles that you solve within a single level, some puzzles that you start in one level and finish in another, and even puzzles that span the entire episode. The puzzles are like Doom's where you find a key to open a door or flip a switch to move something, but since some of the puzzles are so large there's often some kind of a clue that helps you know where to go next. For example, you could find a "fire key" which should be used in a level with a lot of lava, or if you flip a switch in a room full of ice, it probably moved something in the ice world. Sometimes the puzzles are different, like there are stained glass windows that you can break, and behind 3 of them there may be a vial of health, but behind the 4th there's a switch or a long corridor.
The scripted sequences just make things more interesting, like there's a room in a cave where the floor is broken up into a bunch of segments that move up and down randomly, and you have to find a switch, and then when you flip the switch all of the segments move into maze-like position, making you have to find your way out.
I think the most important thing to preserve, though, is the beautiful atmosphere of the levels. It's like a medieval fantasy world with ambient visual effects, like leaves falling from trees. The levels all have themes, like a medieval-looking castle, a dark cave, an ice cavern, a swamp, etc. The levels are also much more detailed than Doom's, even though it runs on the same engine. Basically, a lot more polygons per room help it feel more realistic.
It can be done, and I hope you're up to the challenge, I'm just giving you a heads up that this game is way different from Doom. I'm not sure how I can help, but let me know if you need anything to make HeXen work in Oblige!