Gameplay is not altogether too different from Etrian Odyssey, when it comes down to it. Players are tasked with plumbing the depths of various dungeons, acquiring gold, items, and experience as they do so. It is possible through repetitive journeys into these dungeons to progess further down where a boss will frequently await. Of course, conversely to the main Etrian Odyssey series, the dungeons in EMD are mostly randomized. Each trip will likely be very different from the last. There also isn't much in the way of puzzles or unique exploration mechanics. The ninja class can walk on water to subvert certain obstacles, but it's seldom necessary to think outside the box to progress.
Etrian Mystery Dungeon almost feels like an arcade game with heavy RPG elements. Each of the four characters in your party has a fatigue gauge that gradually drains as you walk around--but it can be replenished with food and by walking over some suspiciously-colored amber tiles scattered throughout the dungeons. These tiles also restore 1 TP apiece, meaning it is possible to sustain very long journeys into the labyrinths. This is good, because the series staple item Ariadne Thread--an item which allows instant return to town--is much more rare this time around. It is only infrequently available to purchase and drops seldom from slain monsters. Combine this issue with the fact that you'll lose all items upon death and you'll run into plenty of frustrating situations and lost progress.
The Etrian Odyssey series has always been punishingly diffcult, but Etrian Mystery Dungeon really ramps it up as far as penalties are concerned. Losing equipped items upon being vanquished is insanely frustrating, particularly when you have gear you've wasted precious armory scrolls on to upgrade. There's no way to restore a previous save to try again, either--because the game automatically saves your progress upon death. You can choose to call your party back and lose precious items, or send a rescue party (comprised of characters you'll also have to have leveled up prevously) to bring them back. Now, assuming your rescue fails, those party members will lose items too. I can't imagine why anyone thought this was a good gameplay concept.
The base game is actually pretty fun, even if the options for character building are thin in comparison to the third and fourth games of the series. The Protector class invalidates most other available strategies due to the game-warping power of Provoke--a taunt that works without fail and consistently protects party members from harm. I couldn't help but be reminded of the imbalanced power of the Protector and Medic classes from the original Etrian Odyssey. I wanted to try the ninja as my "tank"of choice instead, but it would have made the game a lot harder and by a certain point I just wanted to be done with it.
I have mixed feelings about Etrian Mystery Dungeon. I really enjoy the concept--and I do think Etrian Odyssey works in roguelike format--but I think the classes could have been a little more interesting and the dungeons themselves more inventive. I'd jump to try a more polished sequel, though.