The biggest difference, from what I've read, was rewriting the guidance software to discriminate the satellite against the backdrop of space. The SM-3 uses a monochromatic IR seeker to track TBM RVs, which are heated by friction and ablation against the upper reaches of the atmosphere. The satellite was much closer to ambient temperature at the time of intercept.But the projectile size is probably the main issue. Even so, there's only a few factors of ten between a school bus and a warhead. It seems odd that, despite the amount of money that we through at the problem, we STILL can't get it to work.
As far as success rates go, AEGIS BMD does pretty well. Second to Patriot, it is the most mature BMD system in our arsenal. It hasn't suffered the same systems integration issues that Ground-Based Intercept has (the land-based interceptors in California and Alaska). I think the Navy is up to a dozen intercepts now during testing. The most recent ones have involved Japanese warships providing telemetry to the launch ship, and the most recent test had a JMSDF ship firing the SM-3 from its VLS launcher.