1. The Opening Quiz in PMD2.
Okay, I'll admit it, I looked up a quiz walkthrough to get the starter I wanted, but even then, I still had to do the quiz several times. This was because the quiz never gave me enough of the right questions to contribute to the nature I wanted. And every time I had to restart the quiz, I had to sit through that too-long, boring intro movie.
2. I like the dialogue, but there is a bit too much of it at times. It's not so bad when it's informative and meaningful dialogue, but there were times when I just wanted to shout "Get on with it, already!" to my DS. The characters tend to repeat the same things from time to time (this includes both flashbacks and characters just saying things they or other characters said already). As well, the number of times characters state the obvious really gets on my nerves...
Example:
(Flara (1) and Cherri (2) are locked in a gloomy-looking jail cell with heavily barred doors.)
Cherri: Uh, Flara... I think this is... a jail...
(No, really, Cherri?)
3. Aegis Cave.
The Ice dungeon wasn't too bad - it took me only two run-throughs to collect the letters to spell "Ice". The Rock one, though... I had to go through that dungeon at least five times before I had all the proper stones. I had to go through the Rock dungeon so many times, in fact, that by the time I'd collected all the stones to spell "Rock", I'd also collected all the stones to spell "Steel". I was able to completely skip the Steel dungeon.
4. Though I love the monster houses and find the traps bring some excitement to the dungeons, the Grimer traps drive me up the wall. I hate having my entire supply of food ruined just by stepping on a few of these traps - it's especially bad in long dungeons where the apples are sparse. To get around this, I usually have to make my characters eat Grimy Food just before leaving a floor, so that I won't have to put up with the bad side effect of the Grimy Food for long.
5. Escort Missions. My major source of loss of Reviver Seeds. I know they're supposed to be difficult, but they just get flat-out frustrating at times. I hate lugging that fifth wheel around and having to constantly protect it from the dungeon's enemies (which, in most cases, would knock it out in one or two hits if given the chance). I hate having that thing use up one Reviver Seed after another, an item which I usually don't have much of, and which I try to save for my main team members in case of an emergency. Escort missions are great for experience, but I almost always have to restock my Reviver Seed stores after completing one.
6. This isn't really something that can be avoided, but the recruiting of weak Pokemon annoys me. It's expecially bad if my level is high and I'm re-visiting older dungeons. Practically every Pokemon asks to join my team after I defeat them. I try to keep only one of each kind of Pokemon on my team, so all these Pokemon asking to join my team are nothing but an annoyance to me.
(1) Player character in my PMD2 file; a Cyndaquil.
(2) Partner character in my PMD2 file; a Chikorita.