Alternative electron acceptors are being actively explored in order to advance the development of bulk-heterojunction (BHJ) organic solar cells (OSCs). The indene-C60 bisadduct (ICBA) has been regarded as a promising candidate, as it provides high open-circuit voltage in BHJ solar cells; however, the photovoltaic performance of such ICBA-based devices is often inferior when compared to cells with the omnipresent PCBM electron acceptor. Here, by pairing the high performance polymer (FTAZ) as the donor with either PCBM or ICBA as the acceptor, we explore the physical mechanism behind the reduced performance of the ICBA-based device. Time delayed collection field (TDCF) experiments reveal reduced, yet field-independent free charge generation in the FTAZ:ICBA system, explaining the overall lower photocurrent in its cells. Through the analysis of the photoluminescence, photogeneration, and electroluminescence, we find that the lower generation efficiency is neither caused by inefficient exciton splitting, nor do we find evidence for significant energy back-transfer from the CT state to singlet excitons. In fact, the increase in open circuit voltage when replacing PCBM by ICBA is entirely caused by the increase in the CT energy, related to the shift in the LUMO energy, while changes in the radiative and nonradiative recombination losses are nearly absent. On the other hand, space charge limited current (SCLC) and bias-assisted charge extraction (BACE) measurements consistently reveal a severely lower electron mobilitiy in the FTAZ:ICBA blend. Studies of the blends with resonant soft X-ray scattering (R-SoXS), grazing incident wide-angle X-ray scattering (GIWAXS), and scanning transmission X-ray microscopy (STXM) reveal very little differences in the mesoscopic morphology but significantly less nanoscale molecular ordering of the fullerene domains in the ICBA based blends, which we propose as the main cause for the lower generation efficiency and smaller electron mobility. Calculations of the JV curves with an analytical model, using measured values, show good agreement with the experimentally determined JV characteristics, proving that these devices suffer from slow carrier extraction, resulting in significant bimolecular recombination losses. Therefore, this study highlights the importance of high charge carrier mobility for newly synthesized acceptor materials, in addition to having suitable energy levels.