The downside of using an external mic on the 5D2 is overriding the auto gain control. Though it can be done.
My own personal sweet spot, having tried larger and smaller units, is the Zoom H4n. This is a palm-size unit that costs about US$300. The built in mics did a very nice job recording live music (a clarinet quartet) in a concert hall last month, but I suspect you'll want an external condenser shotgun mic for recording nature. A good one costs as much as a good lens.
If possible you'll want to record the sound with the built-in mic in the 5D2, as well, so you can sync the external audio. (I have not tried it, but several of my colleagues swear by Pluraleyes
for syncing external audio tracks or multiple video tracks. It works with Final Cut Pro.)
While you are learning how to capture high quality audio, it helps to remember that audio is a profession, just like photography, and takes years to master. At least, it helps me to remember this when I am totally screwing it up every day.