Tried some Pokémon Omicron a little while back (do Zeta/Omicron count as hacks, or should they be categorized otherwise?). It has many decent ideas for the franchise, a huge range of available Pokémon, different starters (Bellsprout/Magby/Horsea) and a hands down pretty awesome Secret Base system, but in many ways, it shines through that it's not professionally made. Some of the cities look really bland, the route design is so-and-so, and it has several cases of bad spelling and/or grammar. Its attempt at making a darker, more powerful evil team is also only decent at best. And don't even get me started on the music...
Still, it presents several new ideas and concepts I'd really like GameFreak to look at for future games. For instance, the NPC who knows about IVs and how to change them (IV stones, approximately as common as Rare Candies, are scattered throughout the region), or the key items that eventually replace HMs (such as the Machete for Cut or the Dolly for Strength). The game is quite enjoyable, and though I prefer any of the official games over it, it shows a different way of making a Pokémon game - for the better or worse.