I’ve reset my game several times before I finally got a combination I’m good with. Of the 4 times I’ve beaten the main game, 3 of them involved me being Squirtle (best kanto starter) with my 3rd time around being Totodile. And my partners through each of them were Chimchar, Turtwig, Fennekin and currently, Chespin. I gave up on Fennekin once I realized Delphox has a garbage movepool.

MAJOR UPDATE
 
It’s done. Destiny Tower is toast! All 720 Pokémon are now recruited and now the game can truly be considered complete! With good Emeras and the Green Looplet, I was able to destroy the dungeon’s traps! With Sunny Blessing, I crushed the entire dungeon and oneshotted everything!
 
And Hoopa… You’re going to need all the firepower you can for the dungeon.

@Hoopa  
My grinding spot in the story was the Calm Craggy Area. Makes for a great grinding spot. That’s the reason I cheesed Yveltal in the first place and essentially had little to no trouble with the post game. Plus, I am a Grandmaster and already recruited both Yveltal and Zygarde. I made sure to talk to Xerneas beforehand. While I can tackle Destiny Tower now, Arceus isn’t going to have me go there because I don’t have everyone yet. More missions to complete.
 
BTW. How many species do you have? I have 664 out of 720. I am very, very close.

@TheMushroomVestal  
Level 35? Okay that makes sense, my starter is only level 29. That’s a big gap. Oh and Torchic is my starter with Pikachu as my partner. I suppose I have some grinding to do.

@Hoopa  
You’re talking about the Sand Dune of Spirits. It’s the first of THREE dungeons you have to clear in order to get your partner back. It’s only ten floors, and I seriously do recommend you invest your Gold Bars and use the Wonder Mail codes to get Life Seeds and Sitrus Berries to increase your HP. As for why Hoopa disappears from your inventory, the dungeon requires you to clear it solo (at least the first time through it). Be forewarned, as you might know, it’s mostly fire-types and ground-types. Bring about fifteen Reviver Seeds so you don’t struggle constantly. If your starters are fire-types, you may have some trouble with Growlithes and Houndooms, as they might have Flash Fire, so make sure you at least have non-fire type moves. For me, if I found a Houndoom with Flash Fire, I just waved a Petrify Wand and went on my way. A good tactic for dealing with Monster Houses is to go through the room you just came in and let the Pokémon attack you one by one, and that makes dealing with them a lot easier.
 
When I did the dungeon you can’t get past, I actually cleared the dungeon on my first attempt at it. I kid you not, I actually did it. WITH A FENNIKIN AT LEVEL 35! I do not mean to brag though as I was just telling you my experience with the dungeon.
 
The worst is yet to come. Mystery Jungle is right after, and you need to clear it and Purifying Cave to get your partner back. If a Haunter and a Vileplume are right next to each other, you’re completely screwed. Say goodbye to any hope of beating that dungeon now. Yet for me, it wasn’t that tough of a dungeon, as I pretty much steamrolled through it with little trouble.
 
Of course, that would be the worst case scenario, as the dungeon is doable, even with Grass-types. But those damned Ariados will gladly munch away your Reviver Seeds with Bug Bite. Purifying Cave is Psychic and Fairy-types. Thankfully though, you can bring two Pokémon into it, but that won’t help at all as the enemies are much tougher. Oh, and it’s 15 floors. Isn’t that fun? (sarcasm). And if you don’t have any Reviver Seeds? BACK TO THE BEGINNING OF THE DUNGEON FOR YOU! MWAHAHAHA!
 
If you clear all three of these dungeons? Pat yourself on the back and consider yourself lucky. Then you can just clear missions and do everything else, including get all the treasures and increase your rank to Grandmaster.
 
See here for more details.
 
Best of luck to you in these dungeons. I really hope you heed my words and clear these dungeons!
 
So ends the wise words of TheMushroomVestal.

@TheMushroomVestal  
I take it back, the main story is childsplay compared to the crazy difficulty of the post game stuff. Missions are now kicking my ass, and I still cant even do the post game story dungeon (the desert place). I would bring Hoopa but it’s like it disappeared or something (How ironic) Also I would use all level 50s for it, but I think I need my starter to progress the story or something.

@Hoopa  
I settled on Fennekin as my starter and chose Chikorita as my partner. As for the difficulty, I kinda abused Life Seeds and Sitrus Berries at the start of the game with Wonder Mail. At this point, I blasted the Story Mode with an OP Fennekin (because I kept giving her lots and lots of vitamins, which you can usually buy from Cofagrigus for only one Gold Bar each) and toasted Yveltal (the hardest boss in the story mode) on my first attempt, and for people who are about to fight him, PICK AMPHAROS AS YOUR PARTNER! It can save your life. Even Dark Matter stood no chance against me, when people say it’s a difficult boss. Now, I’m taking down the tougher dungeons in the post-game. I always carry around more than 20 Reviver Seeds (which function the exact same as Yggdrasil Leaves in Etrian Mystery Dungeon), so I’m in no danger of dying. I can always get more traveling Pokémon and expand my ranks. I have nearly all the Pokémon in the game. For the Level 5 dungeons, people can always bring Hoopa, who doesn’t get his level lowered, so you can abuse him in the dungeons (but sometimes he will not join the team.
 
P.S. My favorite Pokémon is Gardevoir.

I played this game, it was epic but they were right, it was difficult.

I understand the feeling eventualy I settled on riolu (me) and torchic (partner) although now that I play the post game I sorta wish I had reversed those two simply because of how I’ve tuned each pokemon to complement eachother

@Eeveeinheat  
Well, considering that you and your partner get temporarily transformed into your final evolutions for certain boss battles during the storyline, it’d be impossible to have Eevee be a protagonist character choice.
 
 
@Kerion  
Funny enough, I did end up choosing Treecko for my character with an Oshawott as my partner.
 
Considering the player and partner’s in-game characterization, those two worked surprisingly well.

Not a hard choice for me! ‘Picks Treeko’

@thps48  
I said ‘starter’. Unless you are saying if I beat the game I can reset the save and get a different starter and partner?

@Eeveeinheat  
Actually, Super Mystery Dungeon includes all 600+ Pokémon. Just not all of them available until later… :j

@thps48  
I almost starting bawling my eyes out when I heard Eevee wasn’t a starter. My poor partner Krystal… She grew up to be a beautiful Glaceon. She will never see the light of this game.

I choose Turtwig then choose Froakie as my partner.

@Eeveeinheat  
And introducing a ninth Eeveelution… Or tenth. Nopony remembers. XD

IKR? The least they could have done was make it easy by having Eevee as a choice.

@Rarewarefan  
She hasn’t even gotten to the actual game yet, she’s just stuck deciding on which pokemon to be. XD  

 
…perhaps, but I’d rather not have someone turning it into the next exploitable meme template.  
[…let’s just say that I’ve had past experience with my work being used as fuel for lazy spam COUGHscratchpadwikiCOUGHplagerizedmyfanficCOUGHCOUGH]

I’m reminded of Yahtzee’s review of The Witcher– Or, no, his “First Impressions”. The reason he gave in his video. X3

I saw my family members playing this game. And she wasn’t kidding about it being difficult.
 
(Can we have just an image of Pinkie holding the 3DS without the screenshot please?)

@Jarkes  
The freedom of choice has both a blessing and a curse~
 
A) Quiz chooses for you…you’re unhappy with what you’re stuck with, but it takes the weight of choosing off your shoulders [and there’s a sense that “fate” chose the pokemon]
 
or
 
B) You get to choose…meaning you’re not stuck with what your quiz answers result in; but you’re still left unhappy because you miss out on the other possibilities and then, depending on what you pick, you’ll get limited for your partner choice and may not get the exact dynamic duo pick you wanted. And if you absolutely MUST have your starter or partner mega evolve, that limits you to only 7 options: Bulbasaur, Charmander, Squirtle, Treecko, Torchic, Mudkip or Rilou.

I thought you could play as Zorua

At least you no longer have to do that dumb personality quiz where you have no way of knowing what you’ll end up with without a guide, and if you want to go for a different one you have to sit through the introductory cutscene before the title screen again because you can’t skip that until you’ve actually started a file…
 
That was really annoying about the earlier PMD games.