Oh boy, comparing the art styles between the games.
-Shantae: One of the most beautiful games on the GBC. YMMV on calling it art since it's mostly a bunch of pixel sprites, but for what it is it's very well-done. As a hobbyist spriter myself, I can safely say that putting multiple expressions onto a human character barely 40px high, using a limited colour palette, and making them clear is not an easy task, let alone having to do it for every animated instance in the game. I don't think y'all give this enough credit: of course they're going to pale in comparison to their future projects, but you need to look at it from a "How good was this for its time?" perspective to truly appreciate the effort.
-Risky's Revenge: WayForward's next big entry, and their first attempt in a long time at making a 2D platformer for the current generation. Obviously the pixel art is a major step up, so most of the complaints I've seen have been to the somewhat-awkward art style used for the character portraits. From what I know, WayForward themselves drew the portraits even though their field of expertise was sprite art, and while the art-style portraits weren't great, they were okay for a first attempt.
-Pirate's Curse: For this one, Inti Creates partnered up with WayForward and started handling the non-sprite artwork, allowing them to focus on the sprites and gameplay aesthetics. The only complaint one can direct at the sprites are that they were in the exact same style as Risky's Revenge so they cite a lack of effort, but that doesn't mean there aren't still a plethora of new sprites; indeed, there's a lot of new, charming and awesome animations that make use of the old style. And the new character art is much more expressive and generally better-drawn. The previous two games didn't have bad art, but Pirate's Curse was definitely the series' peak so far.
-Half-Genie Hero: What appears to be happening in this drastic art shift is that WayForward is straying from sprite art, and is instead using 3D worlds with some of Inti Creates' character art and using some Flash-like tween techno-sorcery to animate them. If you've seen Flash animations on places like Newgrounds or have dabbled in Flash yourself, you'll know what tweens are and after seeing how some of those animations turned out might have questioned this design choice. However, Inti Creates and WayForward's combined efforts show us that this kind of animation and medium-blending can be done right and done well, and even in the demo version of Half-Genie Hero it all looks amazing. It makes me look forward to the full game.
tl;dr: Certainly PiCu and HGH have the best art style and animation, but that doesn't mean their predecessors are bad. They were the first games in the series, cut them a little slack.