What is the best C compiler for Amiga?
I had SAS/C and used it on my a500, I had a 250mb hard drive, 6mb of ram and a 28mhz 68000 though.
Later when I moved to an A1200 (2gb hard drive, 48mb of ram and a 50mhz 68030) I found that the geekgadgets fork of gcc produced better code. I suspect that using a cross compiler on the PC is probably equivalent, you'll be able to most of your testing under WinUAE. Which will save you alot of time.
Your first choice will have to be based on target hardware. If you want to be able to run on Kickstart 1.3 then boopsi/MUI is out of the window. IIRC There was a gadtools for 1.3, but I never did any coding with it (or the 2.x+ version). I just remember a hard drive partitioning utility that came with it.
Otherwise you're limited to intuition or doing your own thing, intuition isn't actually that good. Which is why so much software opened it's own screen and had it's own look.
Serial port access should be possible on any Amiga compatible compiler. Either direct hardware banging or accessing through a device. A device is better because it will work if you have extra serial ports. Although you probably don't want to use the commodore supplied serial.device, there are much more optimised ones that I used back in the day (aminet should have them).
I would have thought there was a gdb based debugger you can use. However depending on what you're talking to on the serial port, you might find that debugging changes timing that will affect how your software works anyway. With anything realtime you're better off logging out data and then analysing it.