Ideas

Fog of war: The players can only see certian objects in their view in the game
More bosses like werewolves and big bears.
Looting system for GM help.

A fog of war effect can be added by placing minis mid-way through a scene, or leaving some of the battlemat as black tiles until a certain corner is turned or door is opened.

Werewovles and bears can easily be implemented, I've seen werewolves done as superhero minis coloured grey and there is an existing bear mini. You can make them seem bigger and badder by narrating that they are :P

Loot on the other hand is simply something that breaks the system and slows down combat. I'd rather take time to build my character and progress through the story instead of stopping and rolling after each enemy in order to try and find a better weapon.

Being able to make and upload custom tiles and miniatures, that could be downloaded from a community section of the fabletop main menu.

Having more space as GM for miniatures.

Could it be possible to have up to 8 players + GM? also i agree with lacergunn, the GM doesn't have enough miniature space.

I think sound effects would be pretty cool.
I'm no programmer, but it sounds easier to code than most things too.

It should be similar to the music feature, but instead, does not loop, and is able to play over the music.

But copy pasting the URL for a slash sound effect sounds too tedious, so perhaps let you bind it to a certain word?

For example, typing:
/bind Sheath youtube.com/watch?v=zqujcCbgwkU
would make it so that typing:
/SFX Sheath
Would play the sound effect.

I have another idea, but I think it's better to post it as a different reply.

Custom miniatures also sounds nice, and again, sound easy to code.

It would be a GM-only feature. At the bottom of the miniature page, you could include a plus symbol, and it will let you choose an image file as a mini. Then it takes you back to that window that lets you view your mini's name, and picture. But this time, with a feature to change the size of the little circle at the bottom of minis.

Sure, it can be easily abused, but so can the music system, and besides, players can already link to images. Both features aren't abused as you'd think. The only difference here is that it'd be on the table's board. I believe it'd also be used for more good intentions than bad.

This would also greatly help with updates. The next planned update mostly contains a ton of additional minis, but with custom minis, you won't have to worry about them too much.

Maybe some custom miniature and more slot to save them ?