Gel insert between a neoprene layer and the outer shell protects against brushing and bruising, as gel absorbs kicks and spreads pressure. Gel and neoprene compensate for imperfections in leg and allows for a snug fit.
I could see them being useful if your horse has an old splint that needs some extra cushion so the boot doesn't rub it. But that's it..
I personally like the gel (or memory foam type) front boots (eskadrons, equifits, etc). If you feel them they're very squishy which offers a better fit and can take more impact (thus provide more protection) then then regular neoprene. It's especially nice for a horse that interferes and I figure it's nice to protect your horse's legs as much as you can.