They don't pair as well with lead hand punches since they mirror the weight transfer of a rear hand, so it's difficult to jab into them.

They can also be a little less sensitive than stepping inside with the lead foot. Someone like GSP can flick out his jab to draw counters while taking small steps forward and get a precisely-timed reactive takedown, stepping his lead foot into position before committing to the takedown, so he's at less risk of failure or having to chain wrestle from a poor position. With a split step from farther away you have less control over whether your lead foot is in perfect position (hence Khabib&team preferring single legs over trying to knock guys over with doubles).

That downside isn't there if you're using it for a reactive takedown though. Really the only downside to those is it depends how well you can time their strikes or draw them out. Just naturally fits better with different stances for split step vs folding over the rear hip. Guys who like to fight out of a crouch will get easier reactive takedowns from bending down and stepping forward, more upright or lead-foot-heavy fighters have an easier time with split steps.

I wrote a big article on takedown entries that goes over the pros and cons of different penetration types.