I think it does make a big difference. You should think about what you want to do. I purchased my first Arduino because I wanted to work with the LoL LED shield. I purchased a Leonardo and when it was all put together it did not work because the LoL is not compatible with the Leonardo. I then had to purchase an Uno to get my LoL working.
Now that I have the Due I've been working with devices that I know will work well with it. Most of my latest projects involve using many individual LEDs. The plethora of digital outputs on the Due make complex LED circuits much easier to build and control because you don't need all those shift registers.
My advice is to decide what type of work you want to do. If you want to use a lot of currently available shields and libraries, then get the Uno. If you plan on building all your own circuits and libraries then get the Due.