It isn't always that they were just lazy and skipped over a bunch of stuff to get the games out onto the market RITE NAO. They also don't always make third games for the sake of more moola (though that's not a bad thing).
Yellow, for example, was created to resemble the anime. That's pretty obvious.
Crystal included new features like being able to choose the gender of your trainer, Pokémon sprite animations, the Battle Tower, and some other stuff. A lot of people complained that this wasn't enough to set it apart from G/S.
Emerald also brought back sprite animations. Magma and Aqua had a much bigger part in the storyline as well. New zones were added, there were attack/breeding changes, the Battle Frontier was updated, you could rebattle gym leaders, rare legendaries, contests, etc.
IMO Platinum is the best example of why exactly they make third games. D/P came out on a new system, something they were unfamiliar with when it came to making Pokémon games. In Diamond and Pearl the animations were very slow and choppy, which they fixed in Platinum. They changed small details within the storyline and gameplay with the introduction of Giratina. New Pokémon were added to the Sinnoh 'dex which changed how you built your team. Again, the Battle Frontier was updated, and they added more Wi-Fi compatibility than what was offered in Diamond and Pearl.
Really, the developers sort of go in blindfolded when releasing a new generation, especially if they're on systems that are new to them. They really don't know how the games will be received until they release them, and then they hear the feedback from customers and make adjustments accordingly. The Wi-Fi compatibility was a huge thing with the Nintendo DS, but in Diamond and Pearl the only feature with it was the GTS (besides trading). At the time that was a big deal but it's like...you can do so much more with it. So they allowed Wi-Fi through the Battle Frontier, poffin making, Wi-Fi clubs, sharing battle videos/Pokémon collections, and so on.