But first I wish to address a small issue when it comes to pixelmon adventuring. The lack of challenge. As if you have no conscious pokemon in your party you can continue about your day adventuring with no danger to your pokemon. So i have 2 solutions to this issue. First when a player losses their team they "black out" like in the games and return to their spawn point. Or my second suggestion all natural spawning chests are unable to be used UNLESS a pokemon in the party is conscious. This would add more stakes to adventuring as if you lose it's over and you have to try again. Thus giving adrenaline to adventuring and forcing the player to be more tactical.
The first and most common areas that a player will find are villages, which are very well implemented into the mod with gyms, poke-centers, and poke-marts scattered throughout. As of yet I have no improvements to make to these areas, but I wished to start on a compliment.
Next, i wish to address some of the smaller structures: Fossils, buried treasure, witches hut, and ship wrecks. Fossils should contain actual fossils and so should buried treasure. Witches huts should contain the woodland mansion map, which i'm not sure is obtainable in pixelmon due to the lack of villagers.
Next i wish to talk about three structures that will gain notable importance to pixelmon, these being mineshafts, igloos, and ocean ruins. Each of these should hold fractions of items needed to summon regis (Steel in mineshaft, ice in igloos, and stone in ocean ruins) instead of regis naturally spawning now you have to explore to capture them.
A similar concept would be used in Ocean monuments and Nether fortresses. In each of these I suggest the spawning of "bell shards" for Lugia and Ho-Oh's bells. Each of these should contain a maximum of 2 for a recipe of 8 shards and a string leading to the need to find 4 of each structure to summon the legendaries.
Next the stronghold needs to be addressed. I suggest placing the timespace alter in here as it is a rare structure that requires work to get to it. However I would suggest that that Arceus not be summonable from here, but he rather has his own independent structure in the end. Also the strong hold should only contain weak Unknowns that spawn. When you enter the portal and go to The End you need a strong final boss. So you make it here use the bell and Arceus appears and is rematch-able with another bell.
The villager outpost is a curious area as it still contains hostile mobs in Pixelmon. I would obviously get rid of these and turn it into more of a dungeon. The area should have aggressive evil scientist trainers and dittos. You get to the end and battle a high level trainer get a line that says but you're too late. And here you either have an uncatchable mewtwo fight (similar to SwSh) that rewards you with both mewtwoite X and Y or (I apologize for the upcoming wishful thinking) a shadow-pokemon fight leading to a shadow core as a reward to create a shadow cloning machine letting you create you're own shadow mon, but that is a wishful thinking. (If this were the case I'd have the ditto switched to unknown possibly).
I hope some of these are incoorporated in order to make exploring more of a quest for legendaries rather than staying in a biome for ages to find one.