Obviously, the gamepad is a factor. Sony and Microsoft are also willing to take losses on consoles to grow their install base. Nintendo doesn't do that. Also a factor is the strength of the yen. Nintendo has said several times that they wish to drop the price of the Wii U , but haven't been able to because of the exchange rate.
At this point, it wouldn't make sense for Nintendo to take a loss on the system at all. The Wii U is not a long term proposition anymore. Truthfully, though, they really need to keep the price at $250 going forward, and any cut from there would be beneficial (provided that Nintendo still made a marginal profit on it going forward).
Keep in mind people: the word floating the web is that Nintendo stopped making chips for the Wii U at 20M mark, towards the end of last year. If there is any truth in that, then they really aren't looking to rush their remaining stock out the window at no profit. If they can continue steady sales until the launch of the NX, they will remain profitable and maybe even sell out the whole production run.
In that scenario: they're playing a balancing act. Increase sales incrementally, but don't deplete their stock at any lower profit than is necessary to sell out on schedule.
Max profit over a fixed timetable.