In the last few years there has been a lot of interest in quantum repeater protocols using only atomic ensembles and linear optics. Here we show that the local generation of high-fidelity entangled pairs of atomic excitations, in combination with the use of two-photon detections for long-distance entanglement generation, permits the implementation of a very attractive quantum repeater protocol. Such a repeater is robust with respect to phase fluctuations in the transmission channels, and at the same time achieves higher entanglement generation rates than other protocols using the same ingredients. We propose an efficient method of generating high-fidelity entangled pairs locally, based on the partial readout of the ensemble-based memories. We also discuss the experimental implementation of the proposed protocol.