One thing I've been thinking about is the addition of links that set variables as well as going to passages. Many would agree that this could potentially simplify a number of Twine coding cases.
A proprietary "Twine clone" program called AXMA has this functionality in the form of this extension to the link syntax:

[[Kiss her once|Flower Patch {$kisses = 1}]]
[[Kiss her twice|Flower Patch {$kisses = 2}]]
[[Kiss her four times|Flower Patch {$kisses = 4}]]

As in, an additional parameter after the passage name, enclosed in curly braces, that contains a <<set>>-style declaration. I feel ambiguous about this syntax - it seems like it doesn't mesh with the rest of Twine's syntax, using curly braces just for this one occurrence.

In my mind, I've been turning over a possible alternative, one which continues the use of the pipe character as a separator between parameters of the link syntax:

[[Kiss her once|Flower Patch|$kisses = 1]]
[[Kiss her twice|Flower Patch|$kisses = 2]]
[[Kiss her four times|Flower Patch|$kisses = 4]]

I was thinking of writing a script to add this, but then I noticed that this can be replicated in Twine already, simply by combining my <<insert>> and <<goto>> macros:

<<insert "rush off">><<set $stealth = 0>><<goto "Glasshouse">><<endinsert>>
<<insert "sneak off">><<set $stealth = 1>><<goto "Glasshouse">><<endinsert>>

What I like about this is that it's extensible - any quantity of macros can be placed inside the <<insert>> as long as it finishes with <<goto>>. It also makes use of already extant macros in a clever way.
Of course, its main flaw is that it's altogether a bit too verbose to be used all that often. So, I'm still considering whether to create that link syntax extension, and what form it might take.