I agree with increasing available skills to 10. I have occasionally seen designers complain about being unable to implement an idea they had because of the current limit. Also, it would mean that "crash course" levels (where the first levels of a pack introduce the skills as many at a time as possible) could get through all the skills in only two levels.
I don't like the suggestion to make the minimap variable-sized. It's true that it doesn't cope well with large levels, but there's no reason to think size of level is negatively correlated with number of skill types (if anything, you'd expect to see positive correlation).
Instead, we could get rid of some of the "Korean washing machine" buttons. Directional select can go; it's much more convenient to use a hotkey.
Nuke doesn't have much purpose any more; it's mostly a relic of L1. To namida's argument --
A corrupted or just poorly-set-up hotkey configuration, combined with removing the nuke, could leave a player with no way to terminate gameplay.
-- a simple answer would be to make Escape a non-remappable "exit" key. There might be a problem for new players if we remove the nuke -- they might solve a level but have remaining blockers, and not realise that exiting via Escape will count as solving the level as opposed to aborting it. Still, if we make a new intro pack at some point, it could showcase this exact scenario to teach the use of Escape.
The pause button is also not much needed, because NL has so many levels where assignments must be made precisely, now that framestepping tools allow for this, that moving the mouse down to the pause button is simply too slow most of the time. I somewhat sympathise with namida's point here, though, so if we decide on removing two buttons to allow two more skills, I would go for directional select and nuke, keeping the pause.