A single speed will make your upper body stronger. When you ride a single speed you can't sit and spin your way up a hill, you have to stand up and pull on the bars and use a lot more body english. A rigid fork will make your forearms stronger trying to hang on in rough terrain. Suspension can soak up a little bit of your energy from pedaling but it gives back a lot more when the trail gets rough. So overall, suspension makes riding a mountain bike easier. Gears help you keep in the aerobic zone - without gears you end up going anaerobic. So it would depend on what type of fitness you are going for. You can also increase your fitness level on either type of bike by trying to go faster or riding more.
I think it's mostly about having fun. If you are enjoying yourself, you'll get out and ride more. I mean, you could challenge yourself by trying to ride a 40lb freeride long travel bike without a granny gear up steep hills (you might end up walking a lot) but why would you do that unless you were having fun? I love my single speed and sometimes I put a rigid fork on it. It's my bike of choice for 95% of my local (SF Bay Area) rides. But when I went to Moab this year, I took the full-suspension bike (with gears) because it's more fun when the terrain gets rockier. Yeah, I could have done Porcupine Rim on the single-speed with the rigid fork on it, but I had a lot more fun going full blast on the double-boinger.