Edit 2 July: Finished the whole game! Cleaned it up a bit, and clarified some stuff.
Well, Pokemon Mystery Dungeon Explorers of Time and Darkness haven't been out for a very long time, and thus guides are hard to find. But I just thought I'd post my experiences for people who want to try these two fabulous DS games.
Also thrown in are some general tips, brief comparisons to MD Red and Blue (I've played Red) and if anyone has questions (I've finished most of the main storyline), post them here and I'll answer as best as I can.
(If you need it, I'm also willing to rescue you. PM me.)
I personally find the storyline a lot better than Red and Blue. But don't worry, spoilers will be kept to an absolute minimum.
Just know that it is big, epic and wonderful!
The questions at the start are similar (but not identical) to MD Red and Blue. (I'm a Totodile.) And your partner, like MD Red/Blue, can't be the same type as you. (Mine's a Cyndaquil.) Also, there appears to be more emphasis on gender in this game, it was completely absent from MD Red/Blue but now every Pokemon (including you, your partner, and the Pokemon you catch) have a gender. This is so that Attract can work properly, and whether you are male or female affects what your partner says in the storyline (although this is terribly minor). It also affects the colour of the menu boxes (blue for male, pink for female -and my pink menus are starting to get on my nerves-
but this is equally minor). Also, according to the Prima guide, male Pokemon have a higher critical hit rate, and female Pokemon have higher accuracy.
There are a LOT of Pokemon to catch in MD Time/Darkness. Besides the version exclusives, you can catch/evolve every single Pokemon from all four generations, though some are from hidden/event dungeons. From my personal experience, it is hard if not impossible to beat some of the boss battles (Luxray for instance) without some help from recruits. What I recommend is to pick one Pokemon that you recruit quite early (Starly or Dratini is good, or anything that doesn't stack types with your starter/partner), and bring it with you into the dungeons as much as possible. It will
be a great help.
There are some basic Pokemon not available in the wild (e.g. Diglett and Ekans). You can only get these Pokemon from Eggs that you receive as prizes from missions. The Chansey in town will take care of them for you, but you will of course have to wait a few (in-game, not
real-time) days. So do keep your eyes peeled for missions with ??? as the prize, especially the harder ones. (By the way, the Pokemon that gives you the egg has no bearing on what the egg will be. It is totally random.)
You can evolve Pokemon after you finish the main storyline (after the credits) BUT you cannot evolve yourself or your partner until you recruit Dialga, Palkia, and Manaphy, then wait for another three days to receive the final dungeon from Manaphy. Once it is unlocked, you and your partner can evolve.
As usual, many many items. As well as items from the main games (DP) like Berries and stat boosters, all TMs and HMs are available including two new ones (which will not be named here, but if you get them and read their descriptions you'll see that they can only be used in a Dungeon-like setting). There are also the Dungeon items like bows and orbs (there are some new orbs as well). Speaking of orbs, I advise that you keep a Spurn Orb or a Foe-Hold Orb in your inventory at all times. It will make defeating Monster Houses a LOT easier. Do also keep a Heal Ribbon handy, and a Stamina Band is quite good too. If your Apples turn into Grimy Food, eat them just before a staircase.
A new thing which you might encounter from Foggy Forest onwards are Boxes. Pokemon drop these Boxes when defeated, and the Xatu in town and will open them for you. They have species-specific stat boost items with a rarity of * or **. The Croagunk in the guild basement can swap such treasures for other treasures. Only a few Pokemon have items specific to them, this includes the starters and some wild ones (I have items for Grotle, Happiny, Buizel, and Elekid).
This guide is by no means finished, I will add on more as I discover it. Please feel free to contribute!
Finally, a disclaimer: This guide is typed almost solely based on my own experiences. You may find your experience a little different. But I please ask that you contribute to this based only on your own experiences as well. Thank you.