Proton implanted VCSEL has been demonstrated with good reliability and decent modulation speed up to 1.25 Gb/s. However, kinks in current vs light output (L-I) has been always an issue in the gain-guided proton implant VCSEL.The kink related jitter and noise performance made it difficult to meet 2.5 Gb/s (OC-48) requirement. The kinks in L-I curve can be attributed to non-uniform carrier distribution induced non-uniform gain distribution within emission area. In this paper, the effects of a Ti/ITO transparent over-coating on the proton-implanted AlGaAs/GaAs VCSELs (15um diameter aperture) are investigated. The kinks distribution in L-I characteristics from a 2 inch wafer is greatly improved compared to conventional process. These VCSELs exhibit nearly kink-free L-I output performance with threshold currents ~3 mA, and the slope efficiencies ~ 0.25 W/A. The near-field emission patterns suggest the Ti/ITO over-coating facilitates the current spreading and uniform carrier distribution of the top VCSEL contact thus enhancing the laser performance. Finally, we performed high speed modulation measurement. The eye diagram of proton-implanted VCSELs with Ti/ITO transparent over-coating operating at 2.125 Gb/s with 10mA bias and 9dB extinction ratio shows very clean eye with jitter less than 35 ps.