This question has actually been rattling around in my head for awhile. I enjoy the PMD series, but I've personally felt that the series has gone slightly downhill. There are many things I like about the series, but as the series has progressed, some of those things have been removed.
Red/Blue Rescue - I loved that you were actually playing your story. In the other games, I felt more like a sidekick than anything else. I also loved the Friend Areas. I liked being able to visit the habitats of the different pokemon. Being able to recruit all the pokemon. In the future games, as the numbers went up, the recruitable pokemon decreased, even if only slightly. The rescue base. I liked developing my own rescue base and I thought it was a good feature even if it was only superficial.
Explorers Time/Darkness/Sky - Yes, It had a more involved story which I enjoyed, but like I said, I felt more like a sidekick. I didn't actually feel any link to the character I was supposed to be playing. I also liked the idea of an adventurers guild, but I thought it was wasted. Despite being a part of this world famous guild, after the initial appeal wore off, I found myself being more annoyed with the waking up process of every new day. I definitely loved the addition of the wanted board, especially with magnezone as the police. I also enjoyed the special missions that slowly became available as you were introduced, but as fun as the missions were, I wasn't very attached to many of the characters to begin with.
Gates to Infinity - Decreased amount of starter pokemon, what the hell... I will admit, I was slightly happy that they removed the "magical" quiz that determined your species, because like everyone else, I just reset until I got what I wanted. But seriously, that was a downer. I haven't completed this game yet, but once again, I'm feeling more like a sidekick than a main character. Chargeable DLC... seriously... I've only bought 2 so far, but you're telling me that couldn't have been included with the game. Graphics are great sure. I liked the idea of building your own "paradise", but I typically avoid it because I don't keep track of which stores are which. Then the Hunger... what the hell... I'm not saying it was a great feature, but man did it make me plan ahead before going into a dungeon. I don't even bother taking any items with me into dungeons anymore. Next, reducing your missions to only 1 at a time?!?!? I used to go into dungeons with 4-5 quests under my belt all ranging in difficulties. Now I'm stuck doing 1 and only 1 quest at any given time. The shared experience... I now have absolutely no reason to train any other pokemon, because they're automatically leveled up. I will admit, giving the moves power levels was interesting. Not being able to nickname certain characters... I typically use nicknames to keep track of which pokemon I recruit, and with some of them not nicknamed, my rosters looks weird. Lastly, the V-wheel, I thought that was an interesting feature.
As I said, I enjoy the Mystery Dungeon series, but personally I've felt that the series has progressively gone downhill. That could be one of the causes of the mixed reception that the games receive. If they combined the best features of the series, I think the game quality would vastly improve.
I'm typically inactive between Spring and Fall. I'll be on as often as time allows.