If you're just trying to learn, there's nothing wrong with Atmel or Arduino. The AVR instruction set is easy to follow, and there are good compilers and development environments available.
However, I would not put any Atmel part in a real design unless it were second sourced. About 10 years ago, I was starting up and looking for a controller for a design, and I really wanted to use the Atmel part, but finding them in any quantity was a nightmare. So I went with Microchip, bought a good compiler, and repressed my distaste for the architecture and learned it well. In retrospect, it was a great decision. Microchip parts have long life cycles, and even devices based on obsolete technology (the "C" Eprom parts) are available easily. They have excellent support for large and small customers; ordering preprogrammed parts is easy and robust.
In the course of keeping up to date, I regularly check in on Atmel, and sure enough they continue to fall short. However, the arduino is so easy to use, I picked up several of them just to bang out one-off test rigs, simulators, etc.
If you are designing a product, one thing that is nice to do when deciding on parts is to get on Digikey, Mouser, etc., and do a parametric search, making sure "in stock" and "RoHS" are checked, check your parameters, and sort by descending stock quantity first, then by increasing price. Check on a couple of sites, and on octopart.
You will want to pick the right tools for the job, but ultimately, if you learn a small range of tools to cover the bases, and buy the tools, and learn them, then you will end up going back to just a few architectures, such as (PIC12/16, PIC24, and NXP), or (PIC12/MSP430/ST) so you can hit the ground running every time.
Dave