Here are my problems with seals:
1. You cannot deposit your pokemon into the PC if they have seals. Having to constantly put them off-and-on was too big of an inconvenience.
2. The art was inconsistent with itself. Whereas some effects were sprites/pixelly, others, like the fire, flowers, and musical notes, were gradients or antialiased. They didn't go well together with the sprite feel of the game.
3. Not enough options. We have yellow and green lightning, but no blue lightning. Seriously, green lightning, but no blue?!
4. Seals appear from top-to-down. You can't control the order, or if they appear behind the pokemon.
5. They spelled "seel" wrong durr.
6. In HGSS, you only get 3 random seals as an inconvenient daily. Not worth the effort
My biggest problem... they gave up. They didn't integrate them into the new games, and tried to improve their flaws. No, they just gave up with seals completely. Even Battle Revolution, which debuted in the same generation as seals and would have looked amazing to see alongside 3D effects... didn't have seals. :( Alas, they failed to become a memorable option in the games.