They should put the same analog sticks that are in the pro controllers in them. Those tiny little nubs aren't good enough.

I find the joy cons to be shockingly near perfect the longer I've had the system. If they could improve the fluidity of how the bumpers slide off, get rid of that slight "did I just break it" feel when you take them off. And get rid of the "shit, I definitely broke it" feeling of taking them off when you  put them on wrong. Headphone jack is a good idea also for tabletop like others have mentioned.

I know people who got hurt by removing the straps, good idea

Stronger signal transmitters and better placement for the one in the left joycon.  I also would like to see different types of joycons that open up the doors to whole new formats of play.  They could start a whole new generation of games with the Switch just by releasing a second primary set of joycons with different functionality.  We could end up with genre specific joycon standards depending on how well they work with the games.  Not niche, but essential. Upgrades and versions of Switch will likely change how companies look at console designs going forward, by being component driven.  If done well, this could be industry changing.

There are many fanarts about it

Wireless charging please, so I don't have to snap them on the console/dock every time.