GSC/HGSS are the worst games in the series. They completely mismanaged every advantage they had. Even their positive points were tainted by horrible decisions.
Let's see:
1. The new Pokemon. While there are some solid designs (Espeon, Umbreon, Heracross, etc), most of them are either Baby Pokemon or single stage Dex filler. But the biggest sin is that most of them play second fiddle in their region or they are not even in Johto! They are either only available at night or in the early morning, they are hard to obtain (trade evolutions),annoying to evolve (happiness) or locked into postgame. Nothing like a new game that hides away the largest selling point but throws the common Kanto Pokemon in your face! And the ones that are available largely flounder. Take Ledian. Great design but unusable.
2. Mismanagement of new assets. Sure, Dark and Steel Types expanded the gameplay but good luck using those types in your playthrough. Unlike XY, which proudly showcased the Fairy Type, GSC hides away these two new types. Actually using them to win Johto Badges? Nah. That is a luxury. The cell phone. Great idea. But locking stones behind the cell phone was imbecile. Sell them in the stores. We know how the cell phone works. Same deal with happiness evolution for Espeon and Umbreon. Use the Sun and Moon Stones. Game Freak apparently believed we needed constant reinforcement to remember they invented happiness evolutions. The Bug Catching Content. No Johto Pokemon in it despite debuting several new bugs.
3. The level curve. Enough said.
4. The addition of Kanto. Cool concept but it was an empty shell. Everything unique about Kanto was either stripped or downscaled. Sure, fighting the full teams of the Kanto Gym Leaders was exciting but that could have been done in Johto in some room.
5. Speaking of Gym Leaders. The Johto Leaders used only four Johto Pokemon for no discernible reason. Metapod and Kakuna? Really?!
So much wasted potential.
