Eclipse doesn't properly support Android Gradle projects. The Android plugin has a lot of specialized support for android-library modules that Eclipse's Gradle integration doesn't know about. For the time being, if you want full IDE support for Android/Gradle, Android Studio or IntelliJ with the Android plugin are your only choices.
We know the situation for people who are using the Gradle build system and want to use Eclipse isn't great; it's something we're thinking about, but we don't have anything definite on the roadmap yet.