I actually don't know what the reasons are.
Sonic 06 being remastered would be actually great if they made it a functioning video game. The only real thing I don't like about the game outside of the bugs is Eggman's design and the weird furry plot.
Quest 64 is unpopular enough to not sell. They can't modify the game due to the rights being still held by Imagineer, so saving within the game's own memory card system is harder to work with. Lastly, even if they wanted to improve the game, they can't for the previous reason. A translated version using the Japanese game(Eletale Monsters) would be severely better coding-wise, and balance-wise.
As for 06, Elise falling in love with her hero isn't all that bothersome. It happens. It's not even weird. They're basically regular people. Now the fact she falls in love with hero, while being a princess, and being kidnapped constantly? That's an actual issue with the writing. The uncanny valley design is an issue too. It's just creepy at times and while there's a few good moments(Sonicman) and Eggman's design actually is somewhat neat due to his movements and his glasses with technology inside, it's still very offputting. Then you got the timey-wimey ball and the whole time travel oddness. It doesn't make sense and is confusing as hell.
To say the least, fixing the gameplay is easy. But remaking the plot while still keeping some key things(like Elise being who she is, which makes sense why Eggman is kidnapping her, as well as Mephiles' goal) isn't easy to do. Especially with the various characters and what they do overall. It needs a lot of work.
...Ironically fixing Quest 64(well, bar the plot as even the Gameboy remake didn't make it much better, just added actual characterization/cutscenes) is overall easier, since the story was never really more than a quick NES plot(like Dragon Quest 1) and everything was about the world/lore/gameplay/character designs/unique flavor/music anyway.
