I share your grievances with
Pilotwings 64. It's yet another game from the minds at R&D3 that has been suspiciously absent from Smash for no particular reason, but what really gets me with this particular game is the fact that, unlike the other examples discussed in this thread, it
was released in Japan despite its clear deviance towards western audiences (mostly in its casting of Nester), and as such, I genuinely cannot see why Smash continues to disregard it unless there truly is some sort of stigma with R&D3. It definitely raises some questions about the relationship between Genyo Takeda and Nintendo's management back in the day, since for all we know, these creative conflicts could be part of the reason why R&D3's career as a game developer was cut so short (in fact,
Pilotwings 64 was their final game).
I admit perhaps this all sounds a little conspiracy-like, but
looking at the development team's history and how quickly they shifted from game development despite the creative prowess displayed in the
StarTropics &
Punch-Out series, it's not out of the question that Nintendo may have been unhappy with Takeda's dedication to the western market and wanted to put it to an end. There might be negative connotations with games like
StarTropics as a result.
Of course, there are also other, more optimistic ways you could approach this; Nintendo has been very kind towards the
Punch-Out series in the years since R&D3's game developing days came to end, as we saw with Next Level Games's ambitious reboot on the Wii, and subsequently its inclusion in Smash 4. Perhaps the biggest Smash-related takeaway is Little Mac's appearance as an Assist Trophy in Brawl, since, at that time,
Punch-Out hadn't yet gotten the Japanese exposure it would later see in the Wii reboot and was nearly on a
StarTropics plane of obscurity (for those who don't know, all
Punch-Out games only saw extremely limited release in Japan and didn't have even a fraction of the popularity they did stateside). The fact that it still got an Assist Trophy despite that is very reassuring.
So, assuming in this scenario that there ISN'T an anti-Takeda/western complex at Nintendo, I can only think that the reason why so many western-exclusive or western-tailored first party games are neglected in Smash is just a combined lack of interest and research.
We already know that said research and resources were often pulled from unofficial online sources -- I've done a lot of overseas digging regarding
StarTropics, and every Nintendo-related Wikipedia discography I've ever found makes ZERO mention of either game, even on biographies of Genyo Takeda himself. Aside from the shoddy article dedicated to the first game (there is none on
Zoda's Revenge last time I checked) which would take some major digging to find,
StarTropics might as well not exist to easterners. That the "spirit team" on Ultimate let the game slip by them is not surprising, assuming NOA wasn't involved in spirit research.
Pilotwings 64 still baffles me, though. It definitely has historical importance as one of the two Nintendo 64 launch titles, and despite its underwhelming performance in Japan, it's definitely a well-loved game with a memorable cast of spirit-ready characters. Why it's treated so poorly both in and outside of Smash is beyond me.