The GBA games edge out those on the DS. Well, for the most part- HoD is definitely the worst of all six while OoE is at least in the same league as AoS and CotM.
I'll admit, Circle of the Moon was my first Metroidvania so I may be a little biased here. I really like this game. The castle is large, has a bunch of secrets, and houses some intimidating boss fights. Your character feels weighty and movement around the castle is enjoyable. Enemy placement actually changes depending on your progress, which was a neat touch. The music direction is also excellent, especially for the (albeit few) original tracks- Castlevania could afford to have music that sounds more in line with Fate to Despair and Proof of Blood. Nonetheless, there is a general lack of animation frames and certain enemy sprites are frequently recolored and reused throughout. Some people also criticize the game's palette and how dark it is, but this is something I valued. It worked for this game and seemed appropriate.
Harmony of Dissonance is the only Metroidvania that I sincerely dislike. Juste's design is the worst of all the Belmonts and his spriteset is terrible. The music quality is bad, especially when you consider that this compromise was supposedly done for the visuals, which are gaudy and ugly. Many enemy sprites are simply downgraded Symphony/Rondo designs, the default castle is small and lacks breakable walls and compelling secrets, and the "B" castle is too similar to the original to be all that fun to run through. The plot is pretty ridiculous too- Alucard Belmont's jealous amigo, who happens to be a ninja, is brainwashed by Dracula's dismembered organs and runs off with his girlfriend. Err...
Aria of Sorrow is excellent, plain and simple. Whereas HoD struggled for a cohesive identity and opted to just ape Symphony up front, Aria is a focused experience presentation-wise. Along with many of the enemy types being unique, the game manages to look and sound significantly better than HoD. The castle design is very smart: the game environment is large, varied, and contains little recycling. The plot is also surprisingly ambitious and progressive, especially given the rest of the series. The game also has many things to do/collect, thanks to its weapon and soul systems. It represents a quantum leap over Harmony, in my opinion.
DoS, while an acceptable sequel, is inferior to its predecessor in terms of castle design, art design, and plot. PoR, though fun, really reeks of "Saturday Morning Castlevania". The characters are obnoxious and look terrible, the castle is right up there with Curse of Darkness as one of the worst in the series, and the game shamelessly recycles assets (moreso than the other DS games). Also, it's not as technically sound as the other games- it's more prone to slowdown and crashes.
OoE is generally more somber and, barring some of the townsfolk, has better and more appropriate characterization. The tone definitely does not feel as homogenized as the previous two games due these traits as well as the improved artstyle. Level design can be a mixed bag, as a good portion of the outdoor areas are used at least twice/have blatantly repeating rooms. However, I really like the endgame castle and how dense it is. It's varied, dangerous, and has a bunch of interesting abilities to go after. OoE is also the first Metroidvania since CotM to have any semblance of difficulty to it, which is something that I appreciated.