It's not that people actually think they don't have the freedom to do something wild and break away from the tried and true formula, it's that they just don't want to.
Eh, I think it's a combination of both, really, and as you're a testament to only the latter, I'm a testament to my own case. Back when I was younger, I thought hacking was cool because I could play around with Pokemon. Most people do. Hacking making the games into something of an engine is far less apparent (or appealing) to a Pokemon fan turned prospective hacker.
But as I explored it (and not just me, I see this perspective from a good number of hackers) and, more recently, as hacking's evolved, I've seen that it can do far more. It's at least half of why I want to see non-standard stuff: untapped potential. But as I said, people generally get into it because of the Pokemon, not the capabilities. Whether they see those capabilities or not later on varies, but more often than not I've seen that people stick to what they know because it's what they see hacking as and what Pokemon can be(this is especially apparent in hacks where ideas are uncomfortably fused with or shoehorned into standard conventions). Which makes sense, it's never brought up and the community doesn't really discuss it so why would you break from that- the idea shouldn't even enter your mind. Which is why I think a thread like this is necessary, because regardless of whether they actually do anything with this, it at least creates the thought that they can do more. Hell, they don't even have to break the formula, even smaller deviations can mean a world of freshness to the player.
And yes, when I say Pokemon game, I mean a game with the standard story. I feel like it's as integral to Pokemon as the Pokemon are. And I'd be willing to bet others feel the same.
Some others do, but I disagree, and I'd imagine the creators (or at least Nintendo) wouldn't be completely on board, either. Some of the spin-offs were pretty solid, I'll say that much, but Pokemon Snap and Pokemon Mystery Dungeon wouldn't have sold as well or probably been as enjoyed if they were Animal Safari and Fushigi no Dungeon.
Quite a few people are almost predisposed to like something more simply because it's Pokemon, and the smarter spin-offs take what people like about Pokemon (other than the Pokemon, of course) and apply it to the games. PMD does this with recruitment, Trozei does this with capture and collect, and Snap built on the collectible motif. PMD really only lauded friendship and teams from Pokemon in terms of story, but friendship is pretty standard in general and the teams aren't related the the original games (nor are they ever the antagonists). The reason I point this out is because, on a large scale, Mystery Dungeon was the first great indicator that Pokemon could tell a compelling story. If we couple this with how well received Rescue Rangers was on this very forum, it's pretty telling that even if they consciously regard "get badges, battle team, beat elite four" as what Pokemon is, most fans very much get the same (or a similar) whimsy from other things- things that indeed make Pokemon what it is without relying on those symbols.