transition states are more unstable and therefore are of high energy than intermediates (we can isolate intermediates--by definition, we can't isolate transition states). in the two step reaction you've given, the intermediate would be of lower energy than the transition states and the step in the reaction with the highest activation energy would be the rate determining step.
if a reaction can proceed through two pathways it will take the pathway that is easiest to get through (has the least activation energy in the rate determining step and thus allows more molecules get over the barrier). this is of course assuming that we're dealing with kinetics and not thermodynamics. i'm pretty confident that the pathway with the higher activation energy would also yield the highest energy intermediate as well; but then again, there's always exceptions in science
just my two cents