It seems these two games have many things in common and it isn't surprising that the latest Harvest Moon game for the DS has copied some of the new features introduced in Rune Factory 3.
First, the plot of the games were basically identical. In Rune Factory 3, you have to unite the Univir Village and the Town though RF3 has added many twists like the main character turning into a sheep and is way deeper and dramatic than in HM: Tale of Two Towns.
On the other hand, Tale of Two Towns has the main character unite the bickering villages through participating in the weekly cooking contest.
Rune Factory 2 pioneered the Request system and Rune Factory 3 carried over the new feature. You can do the requests by looking at the town bulletin board. Rune Factory has the Heart Events triggered via the request system.
Tale of Two Towns, was the first harvest moon game to incorporate the request system with slight modifications. Heart Events do not appear as requests and bachelor and bachelorettes with high jealousy points will not post their requests. Plus, different requests has it's own deadline and most of the requests are just "bring me x".
Rune Factory 3 introduced the Dating system where you can invite your favorite girl to a date to one of the four dungeons of the game.
Tale of Two Towns has no dungeon but there are dating spots where you can date with your bachelorettes. Some girls prefer one spot while others may hate that location.
Rune Factory 3 also has Dynamic Weather wherein the weather can change throughout the day unlike in previous Harvest Moon and Rune Factory games where the weather is static. Tale of Two Towns has a simplified dynamic weather: there can only be two weather change in a day.