I'd love to see a side-quest involving a Pokémon archaeologist where you help them discover something. My idea is that there is a route near where ever this archaeologist has set up a base of operation, like a tent or something. Then, you happen to run into the guy's base and you go inside this tent (as it would be completely optional, you wouldn't be forced into a mini-cutscene where you bump into the person) and you see the person hard at work. Then you can interact with him (or her. I'll be saying him, because it's just a habit) and he asks for assistance as he underestimated the wild pokemon presence, or the trainer he called for help never showed up (or some other cliché). If you say yes, the side-quest begins, if you say no, you can agree to help later. So, then you go into the wilderness (with the guy following you) and eventually come up to some ruins (he couldn't get there before because of the tall grass/wild pokemon between his tent and the ruins). You and him go into the ruins and find a cave that leads to footprints of an odd pokemon that no longer exists. The archaeologist then goes nuts (like any would if they find something like this) and starts to collect samples, etc. Of course, you get to help too and collect samples (kinda like how you collected things in the Underground area of Sinnoh, but unlike there, you are given a short list of things to find, nothing too difficult). You two go back to the tent and he discovers that the footprints belong to no known ancient pokemon (so it isn't Kabutops
', Aerodactl's, etc.). He then tells you you can return later, as it will take him time to completely analyze the data. This is where you are able to continue on with the main game/do whatever you want to do as before this point, you HAD to work with the side-quest. The only way to continue would be to leave the tent and come back. Then he tells you that he learned some interesting things about it, and the bones and other things he and you found before pointed to the only possible location in the region where it lived. You and him then pack up the tent and travel there (the ruins, he tells you, was not in its habitat because of some reason and he believes the ancient pokemon could fly and that's how it got there). Once you two arrive to the only possible habitat [maybe halfway across the region], you do the same thing, but the list you are given to find is longer, and once you get all the things and give to him, he once again tells you it will take him time to analyze the data. This is the only other opportunity before the side-quest ends where you can do whatever. When you come back, he tells you that he has narrowed down the location of its habitat to a small mountain and you two go there. After some digging, YOU find a fossil of it. As expected, the Archaeologist goes nuts because this is the "find of the century" or whatever. He then tells you that you should go to the region's Pokemon University (or museum) if you want the fossil [he will need to take the fossil with him to do the rest of the research on it and possibly bring it to life] and to pick up a nice reward for helping his research. Once you get to the University or Museum [whichever the region has] you meet with him in his office and he gives you both a nice sum of money for helping him out and he lets you have the fossil that he brought back to life (he also was the one who got to give it a name). This pokemon isn't a legendary pokemon, but is still a strong one nonetheless.