With... whatever the hell they are doing with the Fire Emblem franchise, I'd rather not get a crossover with Panel de Pon. I don't want to see a game where you can inappropriately touch underage (looking) characters and undress them to their underwear while the camera zooms onto their breasts.
I think a series that would work great for a crossover would be Kirby. Both franchises are bright and cute and Kirby is also no stranger for referencing other series, whether well known or obscure, with most of them being in Dreamland 3. There's Donbe & Hikari (Shin Onigashima) or Chao & Goku (Yuyuki), but also an entire stage based around destroying Metroids with Samus rewarding you at the end for doing so.
I also would've mentioned Yoshi, but the Yoshi games often have unorthodox artstyles, whether it's a pop-up book, crayon or now yarn, this is kinda what's to be expected from that series. In fact, a Yoshi game with normal, Mario-like graphics would be pretty odd nowadays. Kirby on the other hand looks fairly normal most of the time, with a few oddballs happening from time to time.
But what I would really like to see is that they revisit the idea they had with Captain Rainbow. I thought it was nice to give the obscure characters (and Birdo) a day in the spotlight and it had some cute things going on, like the Famicom soldiers wanting to become a beach volleyball team. Just... make it less ugly and actually release it internationally this time. I think a game like Captain Rainbow, but with appealing graphics would help immensely to get people interested in old franchises.
And that turned out way too long again...