Save money and buy both?
The 1st Wave Commando set are all winners. There are more pros than cons with them. When you get to variants, well, that's a different matter. It's like, do you need Sea Ops Duke or Duke w/ Jetpack or Arctic Duke or Quad Duke or the upcoming, ultra-cool HALO Duke? You get v1 of them, you don't really have to worry too much about the 'other' versions that come out.
I'll break it down right quick.
Duke.
Pro. Comes w/ double holster and 2 ultra-cool pistols.
Pro. He has a great vest that you can attach his grenades to.
Con. The lack of pants. He looks funny with a big vest and chicken legs, same way as Destro. But THAT can be remedied by buying a Duke w/ Jetpack and giving Duke lightwing the vest.

My next Duke will be HALO Duke in which he looks like Master Chief of Halo.
Heavy Duty.
Pro. Comes w/ a huge gattler that has spring loaded barrel action.
Pro. Bandana comes off.
Pro. Has pants. lol
Pro. He's physically HUGE.
Con. Limited poseability w/ gun.
Spirit.
Pro. Has pants. Can be argued that he looks ok w/o.
Pro. Has an interesting bow that can fire arrows.
Pro. Great design and sculpt.
Con. No gun.
Snake Eyes.
Pro. Comes w/ multiple visors.
Pro. His swords turn into tonfa, his sheaths can attach to his back and he comes w/ an uzi w/ a removable clip.
Pro. Great poseability.
Con. He's anorexic looking?
Storm Shadow.
Pro. Ninja bad guy.
Pro. Someone for Snake Eyes to beat up on. Or vice versa.
Pro. Doesn't have a Sigma suit which means he relies on actual skill and strength to fight!
Pro. Comes w/ a stand to hold his swords.
Con. Fairly boring figure.