It's no secret, I really don't like using tools to run agile projects. More than that, in my opinion giving an inexperienced agile team an "agile tool" is like giving a toddler a chainsaw - it's going to end badly. Give me index cards, pens and a whiteboard anyday.
Allan Kelly has beaten me to blogging about tools - and hit upon an interesting anecdote from Jack Kilby, inventor of the silicon chip. Basically Jack believes that the replacement of the slide rule with calculators has taken something away from engineering. Intuition. Using a tool (the calculator) distanced the engineer from needing to know what he was doing (the calculation). As someone who has used both calculator and slide rule, I tend to agree.
And here lies the problem with agile tools.
Using complex tools takes away a basal intuition about what you are trying to do. You lose that indefinable "connection" with the product. You might even say you lose the craftmanship. Another illustration might be the difference between bland, machined furniture and furniture that has been hand crafted by skilled cabinet makers - building 'by hand' copes effortlessly with the small, unexpected imperfections that rigid machine programs do not cope well with, resulting in a more polished product. That's not to say the cabinet makers don't use the occasional power drill or sander - but they understand when it is appropriate.
So stick with cards and pens at first until you understand when using tools (and which one!) is appropriate. Keep you intuition intact. Your product will be better for it.