Who ever said it had to be like a Pokemon game? Is there some unwritten law that every hack every made must stick to the original formula or else it is instantly not good? Why is it so important that a hack emulate the style of the original games? Isn't it up to the hacker what their game will be like? Also, what would be the point of hacking if you are going to make a carbon copy of the Nintendo games every time anyways? And like I said earlier, it will still have a Pokemon engine running it, therefore (so long as there are Pokemon) it will be a Pokemon game. I just don't understand why every game has to be "get these badges and beat super strong trainers while putting data in this machine that, despite being around for years and likely completed before, we refuse to give you anything but a blank one. Also, watch out for the petty evil team who usually have an illogical goal and are often not competent enough to pose a big enough threat to get the police or the military involved. Even my favorite teams- Plasma and Galactic, who are my favorites because they got the closest to doing something, were still defeated by a single kid. Seriously, how does one kid bring down an entire crime organization by beating them in Pokemon battles? Can't the team just heal their Pokemon and go about their business?)
This is why I feel we need more games that don't follow the original formula. Yeah, they're harder to make, but it can be done. (Rescue Rangers, anyone? Although I never played through the entire thing and the part that I did play to I couldn't say that I especially liked it, it is still an example of a Pokemon hack that wasn't exactly like the originals.) If we do get a couple more good hacks that aren't like the regular Pokemon games, maybe it will be enough to break the way of thinking that every Pokemon hack has to be like the original Pokemon games. Nothing has to be overhauled, there can still be trainers and everything, but just doing a couple things differently can have a huge effect.
One thing you can do is Remove Gyms/Make Gyms a secondary goal
Most of the time, gyms in Pokemon games are the main focus, and going to these gyms is usually what leads you to the evil team, which is usually a secondary focus. And if you are going to have gyms, don't do what B/W did. I loved those games, but the regions was just so linear and they had a gym in every town, it made the game go by too fast. B/W may have my favorite story, but Unova has probably some of the worst region design I've seen. The towns are nice and everything, but just the placement of them wasn't exactly good. I liked what Hoenn did, even though it didn't allow for much freedom. It had you do a lot of going around, defeated the teams in certain places before you could continue on. (I'm talking more specifically of how you have to go to Fallarbor and defeat the grunts at Meteor Cave or whatever it is called before you can get to Lavairidge. All the way you had to do a bit of backtracking, but overall the region was able to pack quite a bit of content into a small area.
Also, don't be afraid to mess around with the formula. For example, the games say you have to beat eight gyms, maybe you say they must beat ten, or sixteen. Since apparently ROMs are big enough to support two regions, you could combine them together and make some huge super region. (Sure, the gyms past the eighth one wouldn't have badges, but whatever)
I thought I had more to say, but I don't. Guess that's a good thing though, got out my rant for the day.