I've only been using C2 for a few months and am massively impressed by what it has to offer. It's a big improvement over Stencyl, which I used previously. There are however a few things which I find are missing in C2:
1. More collision control
Stencyl has far more control over the collisions. In C2 it's limited to 'Colliding Yes/No?'. Overlap can be used creatively to solve a lot of this simplicity, but it shouldn't take multiple objects and event code to check for a collision specifically on the left side of an object. So more complexity in terms of actions/conditions for collision would strangely make our lives a lot easier. Another thing that Stencyl does well with collisions is that it groups colliders and allows more of them per object. This can be used to for example have a separate collider for the player's interaction with the terrain and one for interaction with enemies. Often you would want those to be different sizes or even shapes. The terrain collider needs to be wide, to for example allow players to easily land on ledges. The enemy collider however is generally made a bit smaller, to give the player a bit more leeway when close to enemies. This is possible in C2, but requires a lot of events, objects and pinning. It could be so much simpler.
2. Easier individual object targeting
If you want ten objects to each target other objects for some sort of action you need to write a targeting event and use number of text variables to set the targets in the level editor. If there was some sort of object variable, the number/text matching for targeting would be unnecessary and would make everything go a lot quicker.
3. A useful lighting/shadow system
The current implementation of lighting and shadows are pretty bad/useless. Light and shadows never stops, which is kind of the only thing that matters for most implementations. The shadows look terrible and if they don't they have terrible performance. A decent light/shadow system could make a lot of games work more intuitively and look much better. Just look at Thomas Was Alone or Monaco what difference the light/shadows make there.