I could put Dragon Quest 5 in this category. While I did enjoy the game (especially the DS version, which fixed some of the issues), it still has some issues, and I consider the game to be overrated.

In particular:

Issues fixed in the DS (and presumably PS2) versions:
Party size of only 3 characters (why did they do that?)
Return/Zoom fails in many of the places that you would expect it to work (even wasting your MP)
Game can be too easy at times

Issues not fixed:
Monster recruiting too RNG dependent. (Having to rely on RNG for getting a party member is not my idea of fun.)
Magic is underused in this game. Early on, you don't get good spellcasters. Later on, the game balance favors physical attacks. (I can even think of a spell (Crack in DS version) that is unavailable in the original, and in the PS2 version isn't available until *well* after the point of the game that it is a viable option.) (The original had the Echoing Hat, which alleviates this problem end game, but that was removed in the remakes.)
Game is more cutscene heavy than most DQ games.
From a feminist perspective, this game is considerably worse than its predecessor. No option to play a female character, and the female characters that do appear seem to have no role other than being the main character's (potential) wife/daughter. (Notice how the protagonist's son is crucial to the plot and has unique powerful equipment, while that's not the case for the daughter.) Contrast this to the strong female characters in DQ4.

Sonic Chronicles: The Dark Brotherhood - I suppose BioWare did the best they could within the constraints...
Fallout 3 - A janky mess of a game, but it can also be pretty enjoyable when you get into it.
Puzzle Kingdoms - Like a more boring version of Puzzle Quest.
Penny Arcade's On the Rain-Slick Precipice of Darkness 4- Worse than the first two, better than the third.
Mr. Robot - Novel and fun, but ultimately not that special. Also, it ends abrup

Interesting thread since these are the kind of games that we tend to forget.
Anyways here's my top 5 (in no particular order):

Gothic 3- Didn't really click with me. Got bored quite easily.

Two Worlds 2- This is on the list mainly because I played a melee character. It would probably be more fun with a caster.

Fallout 3- I felt it was a bit bland. Vastly surpassed by Fallout New Vegas.

Deus Ex Human revolution- I wanted to love this game, I really did, but the boss battles ruined it for me.

Shadowrun returns- I really like the game (and I loved Dragonfall) but the second half felt a bit disjointed. I think it would be better if the story stopped after the funeral.

To me 'middle RPG' translates into 'at least worthy of one playthrough'.

In no specific order:
* Fallout 3
* Fallout New Vegas
* Dragon Age Origins
* Dragon's Dogma
* Kingdoms of Amalur

I agree with the ones provided above, Two Worlds series is a good example. I found the first better than the second, the second needs the worldmerge mod, and the ending is just annoying.

I would put Risen in here too, it was good, but nothing special.

Its difficult trying to categorise the thousands of RPG's I have played over the years, hell a vast amount I can barely remember.