Indiana University-Purdue University Indianapolis (IUPUI) / Finite element analysis (FEA) in implantology is performed in design applications concerning the complex topology of an implant, according to theoretical assumptions about and clinical data concerning the biomechanical nature of skeletal tissue. Implants are placed in topologically and physiologically complex sites, and major disagreement exists in literature about various aspects concerning their modeling and analysis. Current research seeks to improve the implementation of an implant by the use of short implants, which negate the necessity of additional surgical procedures in regions of limited bone height. However, short implants with large crown heights introduce biomechanical complications associated with increased stress and strain distributions in skeletal tissue, which may cause bone loss and implant failure. The short implant is characterized by the geometric ratio of the crown height to the implant length, called the crown-to-implant (C/I) ratio. In this work nonlinear FEA was performed to investigate the effects and significance of the C/I ratio on long-term implant stability. A finite element model was developed according to literature, and emulation of previous research and comparison of reported results were performed. Comparison of results demonstrated significant sources of error in previous research, which are argued to be caused by mesh-dependency from common model idealizations in literature. A convergence test was then performed, which verified the mesh-dependency of results and challenged the reliability of some common model assumptions and methods of analysis in literature. A 16-point design of experiments was then performed to evaluate the significance and influence of the C/I ratio, considering a proposed novel method for evaluating results and predicting long-term stability. Analysis of results demonstrated that the C/I ratio augments the inherent biomechanical effects of an implant design, particularly overloading strain concentrations at implant interface features. The use of short implants with high C/I ratios is determined to be inadvisable, considering the physiological response of tissue to strain distributions and biological context. A novel, multiscale material model is then proposed to describe the short-term accumulation of damage and biomechanical remodeling response in orthotropic skeletal tissue, as a potential solution to the mesh-dependency of results.