-Battle Frontier: 7 facilities, beat 6 and you unlock the 7th.
-Underground AND overground Secret Bases with the ability the Streetpass bases, and you can leave Pokeballs, items and a "guard" Pokemon for people to take and battle, also they can battle you in the base. Oh yeah, online stuff too.
-Super Contests merging Musicals with the dancing round and Contest Battles. And wifi.
-More sub-quests like the Lost Item thing, the painful time-wasting was SO worth it.
-Entralink + Funfest to merge please, I loved BW's Entralink and was annoyed that it was changed rather than expanded upon, so hopefully we'll have an online Entralink with Funfest Missions.
-More Battle Subway with wifi.
-More areas like Black Tower/White Treehollow. With wifi co-op.
-PWT with Elite Four and more Battle Points as a reward... With wifi.
It's already been said, but I think the Safari Zone was one of the better side-quests in the game. Its randomness was frustrating at times, yes, but it also allowed you to take a nice break from the storyline grinding while giving you new Pokemon to (hopefully) catch.
I personally don't like the contests or the Beauty Pageant-ish stuff. Even the Pokestar Studios part of B2W2 was sort of pointless for me. At least in the Safari Zone, I got rewarded for the time I spent doing it.
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I rarely do the side-quests during the main-quest because I like to finish it in one go without interruptions. But the more side-quests that pop up, the more stuff I have to check out and do when I'm finished with the main-quest. I especially spend a lot of time at battle facilities so I hope they have one of those and hopefully with a rental mode and something fun and challenging like the PWT. A Safari Zone could be fun but I want them to do something more fun and interesting with it and hopefully not the blocks thing like with the Johto Safari Zone in HG/SS. Wasn't really a fan of that.
I'm really hoping for a lot of sidequests. I usually delay my progress in the game just to complete those, and boy, it takes some time. I'd like if some old features could come back improved:
Customizable Safari Zone from HG/SS (Hopefully, several Safari Zones, each one located in their own region, with a ferry service taking you to Cianwood/Lilycove/Fuchsia etc.)
Pokémon Contests (They would be way better if there were just the 4 contest levels, and letting you enter with any type of pokémon; the judges would base your performance on how well you dress up your pokémon matching it's characteristics, and use moves that brings out their beuty/coolness/etc)
Pokéathlon (Or anything using the touch screen; just making it so you don't need to enter all the existent pokémon if you want to get all medals)
Pokéstar Studios (I just don't like how easy it is to screw up during the filming...)
Medall Rally (I have more fun collecting medals than pokémon themselves, and I know I'm not the only one)
Secret Bases (Customization is King)
All I wish (and sadly, I know it won't happen) is for the possibility of doing the multiplayer sidequests using the wi-fi, not only local connection. It may work well in Japan (and maybe some other places), but not everywhere.
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-Lansat, Starf and Enigma berries;
-Burn Drive, Shock Drive;
-Hidden ability Pikachu.
I really enjoyed the Pokeathlon. It's probably my favourite of any side quest. The safari zone (or equivalent) should be present in every Pokemon game in my opinion so I'd like to see that too.
Oh and PWT. That s*** is epic.
Those three would be amazing to have in one game.
I think that the Game Corner will return as the Arcade, and will have many different games instead of just one. That would be amazing to see. As for the Contests/Musical, I think that they will be implemented into the aftergame as part of Nimbasa City, (yes, I am hoping Unova will return.) and the Safari Zone will replace the Nature Preserve. There might be other sidequests like the Entralink and Join Avenue, but I don't really see that happening.
I would like them to shift TMs to be rewards for whatever side quests they do give out, and having less of them simply available to be bought from a selection. That they're nfinite use now gives the opportunity to spread them around and make each individual TM a unique task to obtain; like Pieces of heart, for instance.
I want the return of the Battle Frontier, though I never personally enjoyed it. The Safari was also fun but I'd like a brand new side-quest as well. I enjoyed Super Contests but they feel like a Sinnoh-specific thing to me.
I want the Game Corner back. And it better be a gambling game. I hated Voltorb Flip so much. It would've been one thing if the Voltorb's had to be consecutive, but when it comes down to it, Voltorb Flip relied too heavily on luck with to little payout.
As for the main sidequests, I'd like either Contests or the Pokeathlon. I really hated Musicals and the movie thing lost my interest after about two shoots.
I want the Trick House back too. Was I the only person who absolutely loved that? Oh, and secret bases!
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I love the sidequests oh-so much and I really hope there will be more than one to choose from! Especially contests--I always liked contests, i found them to be entertaining in a derpy way. Really I have no qualms with any side quest as long as it wastes my time!