So there's a lot to consider when it comes to choices.
Choices over 2 unknowns (right or left door of mystery) aren't really choices.
Choices that are inherently obvious to be avoided or taken aren't really choices. You're not going to kill the person sitting next to you right now and you're likely to continue breathing, rather than hold your breath until you pass out.
What that then leaves is all the other situations. For a relatively simple "orc" encounter, there's actually 6 different choices the party could make:
Fight: pretty obvious and expected outcome
Flee: always a possibility
Talk: diplomacy and other stuff
Sneak: try to hide or use stealth to avoid the encounter
Trick: by wit or magic, the players do something clever to get past the orcs
Nothing: surrender or just wait for the orcs to do stuff
I'm being overly generalized here, but that's the point. The exact choice of to use a sword or bow is a micro decision. While it has bearing on the outcome, it's not exactly rocket science to decide what happens next as a GM.
It's the other 5 choice types that some GMs stumble over or even fail to acknowledge during the encounter design. the Trick path opens up a bunch of stuff, including whether the encounter features elements to block certain tricks.
But lets back it up some, because that granularity will mainly help you design/consider an encounter.
If you consider an adventure a linear thing (which, after its done, the telling of it is), there's a number of pretty high level decision points, choices as it were.
To Undertake the quest?
The method of travel to get there?
The tools and solution types availble to solve the quest?
the approach taken to finish the quest?
Once you start making a flow chart, you can see how some choices don't have to matter in regards to the main goal. Regardless of the method used, the DM can easily describe how that method results in the party getting to their destination.
The two points I want to make from this is, as you document a linear "obvious path" identify where some choices could be made, and provide alternatives. Particularly important is to provide information and opportunity for those choices. It matters not that there is a portal in the Lizardman Swamp if the PCs don't know about it.
Nextly, the real value of choices is in what happens next. What meaning and impact do you make that choice carry. I can easily provide my PCs 3 choices of travel, and make all of them interesting, but ultimately not really impactful on the final outcome. Or, I could see that a choice was made, and attach more meaning and siginfigance to that choice.