I've found the TI MSP-430 fairly good as a cheaper/rawer alternative to Arduino. It comes with Eclipse based tooling to program the microcontrollers in C or assembly.
It should also be noted that the msp starter kit is only ~4 bucks and has a full usb starter board with i/o breakouts. pretty cool stuff.
the big advantage of the arduino is the software and the community.
edit: I should also mention the program mspdebug which is a little simpler than gdb. I actually didn't look at this program much after seeing it could let me use gdb but I just looked it over a bit more and it also lets you step, set breakpoints, set registers, and more.
Many jobs we wish to use the timer for can be done in other ways, and many jobs that need the timer can timeshare resources.