I feel like Crystal was the first game to be, like, a third game with actual changes (like Platinum and Giratina, Emerald and the new cutscenes, etc.). Technically Yellow did it, too, but Yellow was my first Pokemon game, and I only played Red/Blue long afterwards, so for me it was something special. It was also the first time that you could be a female trainer, and the first time that Pokemon moved, and the first for a lot of things. I think that's what makes it so special, in my opinion. It was a game-changer in a lot of ways and I feel like people will fondly remember that. It's probably why Crystal is looked back at with affection a lot of the time. Even for later generations with different third games, Crystal was unique because it was the first one to do it (well, Yellow, but I feel like a lot of peoples' first Pokemon games were probably GSC anyway).
So while retrospectively it doesn't look like a game that has all that many special features, at least compared to other, newer Pokemon games, it was one of the first to really switch things up in a way we weren't really expecting as kids (Pokemon moving is taken for granted now, but in Crystal in the year 2000, our tiny minds were BLOWN). That's probably why it's so fondly looked back upon.
And then of course, like VisionofMilotic said, there's going to be even more new content, which just makes it even more worth getting on the virtual console, in addition to all the nostalgic feelings about it.
