Walmart, Best Buy, Circuit City etc. are not at all likely to try to keep Nintendo out of their stores due to bundles, they don't really care, and if they have it, do you really think Gamestop is going to try to? They wouldn't risk losing the sales, so no I don't see how they have any say in that matter.
The only way that they could excert that power is if all stores tried to pull that, and if Walmart isn't going to then no other comapny will, at least not in the US. Don't know about the UK or Canada, but if big box stores keep them in stock then the samller game stores will do it also.