I wouldn't say they're clunky.
Rune Factory was a brand new idea, yet even the first one was amazingly well put together.
Rune Factory 2 had a ton of experimentation on the social side, not all of which worked out well. Some of the structuring changes and shifts to the social interactions really didn't work out for the best. Also, I feel like this game has the poorest characterization of the trio.
Rune Factory 3, however, is simply an absolutely phenomenal game. Its gameplay changes all work flawlessly, the world is great, the characters are lovable, the story is intriguing. It is a great, great game.
The story of the RF games is only loosely interconnected by a recurring theme and a few recurring characters. The worlds share a mythology and history that definitely connects, and from that a fan would have a good idea of what's coming next: (SPOILER)Fourth dragon, Ventuswill, dragon god of Wind, baby!
But you don't need to play the others to enjoy RF3, and you should play RF3, as it is one of the best games on the DS. Its skill system is incredible, similar to Skyrim's, but better executed. Its characters are nearly all brilliant, and all have an incredible level of detail put into them (as in, each potential marriage candidate actually has an entire sub-story that plays out after you marry them of how their married life is going, and how they're relating to the changes in the town, even though you can only marry one character per save file, and these stories take months, if not longer, to tell).
Really, play RF3, it's fantastic.
And I am so psyched about RF4. Bring it on!