Yes, there are loops - while loops, for loops, foreach loops, ordered loops, it's all there.
There are also functions now, albeit a bit primitive since they aren't first class citizens, and they don't really know what scope is.
It is possible to organize your code, and I personally am always trying to steer scirra towards improving the event system to make things more manageable (I think this is way more important than cocoonjs/awesomium/windows 8/etc, but they have to make money), and it's not like they're slacking - the newest additions are containers and functions, and they work well enough (though they could be improved a lot).
Writing plugins may be more work than cramming a solution inside your own engine, but it's not that much work, the cost of writing an engine is gigantic, and the end result if you do write a construct plugin is an extremely modular piece of code that can be shared with the community and reused in other projects.
I used to think it was a bother writing custom plugins for every little thing, but now I honestly think it's worth it.