At the end of the day, I honestly believe that other than their guest appearence in Super Smash Bros that Banjo-Kazooie is gonna come back on a Nintendo platform one way or another.
Most Unlikely: Rare Replay (Nintendo Switch)
Everyone wants to see this happen, Even better would be if they included all the Rareware Donkey Kong games and possibly Star Fox Adventures, Hell I think many would still by a neutered version of Rare Replay even if they had to cut out the Xbox era games due to emulation problems, I would buy it day 1 and wouldn't even mind the Nintendo/Switch tax, But just like I mentioned before the biggest issue has to be the Xbox emulation and how Rare Replay has so many seperate games installed different ways into one package (Pre-N64 games are on the disk, N64 XBLA ports are separate downloads excluding Conker and JFG, Xbox 360 are also seperate downloads), I'm sure it's not impossible, But I wonder if Microsoft would go through the trouble porting it and if Nintendo would collaborate with DK.
Likely: Rareware games on the N64 Classic.
After Nintendo, Rareware probably played the most vital role for them during the N64 era when most developers jumped ship to Sony's Playstation, While it's definitely possible for Nintendo to play it safe and make a game lineup without Rareware's library, It would still feel neutered, decimated and most importantly ignoring a big chapter of Nintendo history's. The biggest question is not "If" ? ,But "When" ? I still feel just like the NES and the SNES the N64 will eventually get the "Classic" treatment, During the Wii U era, Nintendo struggled to consistently release 1st Party games on schedule and towards the end of that era they held back Wii U development in anticipation of the Nintendo Switch seeing how the system was a lost cause, So to pad out the holiday season in 2016 they released the NES Classic Edition which was a success and it was only natural to follow it up with the SNES and the return of the NES in late 2017 due to poular demand, Now that the Switch is sellling like hot cakes, I kind of feel like they will only break out the N64 Classic if needed to pad out a weak release schedule namely during the holiday season, But for now Nintendo will keep that product in reserve.
Most Likely: Banjo-Kazooie and Banjo-Tooie XBLA ports available on Nintendo's eShop.
To concide with Banjo-Kazooie's long awaited Super Smash Bros debut, Microsoft will release both N64 games on Nintendo's digital store, This is an easy decision that takes very little effort on both Nintendo and Microsoft's end, Advertising the Duo via Super Smash Bros will cater towards longtime fans who grew up with Banjo-Kazooie on the N64 and attract young and new fans who haven't experienced these classics and want to see what all the buzz is about.
I will be happy with any of these possiblities and I'm sure one if not more are bound to happen, Of course I will be disappointed if they don't take advantage of the hype/momentum of Banjo-Kazooie joining Smash, But we should consider ourselves lucky and thankful that Nintendo and Microsoft are playing ball to even make this a possibility.
I would prefer Rare Replay on Nintendo Switch and Rareware on N64 Classic Edition seeing how they will be available physically, But will still happily take Banjo-Kazooie and Banjo-Tooie on the eShop as a consolation prize if that's all we got.