Studio 5 has the following problems:
No reference manual/comprehensive help for Studio 5 and C language.
Doesn't it use AVR-GCC?
No command line information for compiler operation, linking, output files, switches.
Isn't it configurable through some menu on the IDE?
No access to a list file after compilation, just the target .hex file.
Again, not configurable through the IDE? Does AVR-GCC produce such files?
Compiler will not report that compilation has stopped at a point in code if a programming error caused by roll-over of a variable causes an endless loop...instead it compiles seemingly without error and produces the same .hex file without changes, even after any program change beyond the point in the program that caused an infinite loop. Compiler reports no problem...successful compilation.
Does AVR-GCC do that? For that matter, does any of the microcontroller compilers do that?
Studio5 requires an expensive debugger card to even begin any type of debugging, such as simply stepping into the compiled program to look at program flow.
The JTAG interface? I actually think it is a cheap debugger card. A card of that type for Siemens PLCs runs at around 400 euro. Plus, a few years ago, it was more expensive.
Otherwise, I don't know how to bitwise address port pins.
You can always create a macro to change pins or, if this bothers you so much, you can always download a shareware version of Codevision AVR and use the limited amount of code and examples, or buy a license for the whole thing. However, from previous experience, I didn't manage to run code compiled from it with the bootloader. Only on a bare chip.
That one will have the "." notation for the registers and a setup interface menu (ahhh, that is actually good) for you to setup the microcontrollers hardware.