I want to have a trained Smash Amiibo of every character. I'm not just collecting them, I want to train all of them. If I used to the Smash Bowser for Mario Party, I would not be able to train it without deleting the Mario Party data.
Also why would the Smash Bowser be more common? Nintendo said the Mario line would be stocked better in general, and I don't see why the SM Bowser would be rare at all. If anything, I expect the Smash version to start getting phased out in a couple of months.
Speaking of Mario Party and Amiibos:
So far, these will be the only Amiibos compatible with MP10. While they could just patch in support for other characters like Waluigi and Daisy, there currently is no Amiibo functionality specific to them. Them being playable in Mario Party 10 does not necessarily confirm them as getting Amiibos at this moment in time.