A "better" way? That's subjective. Your code will likely be smaller, faster, and more efficient. But far more complex since you have to do everything yourself like setting up timers and registers, and such. If you use libraries over there, you run into the same issue anyway (though it will still likely be smaller code).
Arduino is great because it is simple and does a ton of work for you and hides all the really scary bits. But you sacrifice on code size. You are trading some things for another. In the end, you can actually just write the same code in the arduino IDE as you can in AVRStudio. Both are using avr-gcc as the compiler. You can access everything directly if you want.
I think you need to be clear whether you're referring to the Arduino IDE or the Arduino runtime libraries.
There are various things about the IDE that really irritate me. But it's good enough to get the job done.
There are other IDEs that you can use to write sketches and these can make use of the identical Arduino runtime libraries and the hardware abstraction that these libraries provide. Or you could write the source in any text editor and build the image manually - you don't *have* to use an IDE.
It's also possible, as you suggest, you avoid the Arduino runtime libraries completely and write your own code that interfaces directly with the hardware. For people already familiar with working in this environment, that would be a reasonable solution. But the Arduino runtime library does take away a lot of the pain and complexity of dealing with the hardware and if you aren't certain whether you need it then I'd suggest the answer is that you do. But you can use the Arduino runtime library without using the Arduino IDE, if you want.
Possible alternative IDEs are the AVR IDE, Eclipse and Visual Studio. No doubt there are others too. If you're already familiar with any of them, you might want to search for explanations of how to use these to build Arduino sketches.