Mountain bikes can be as comfortable as any other. With slicks they actually ride more comfortably than most because they generally have more cushioning from the tyres.
I have both mountain bike and cruiser. The cruiser is a bit faster and lighter on the road (I have a BSO mountain bike), but in terms of comfort I don't notice a difference. The mountain bike takes bumps/potholes better, skids better and is basically more forgiving for a rough rider on the road and up and down curbs. However with ANY sort of offroad I notice a big difference in favour of the mountain bike.
In saying that, my mountain bike is a 29'er hardtail, I don't feel comfortable on the smaller wheeled mountain bikes, but that might be just a matter of practice. The bigger wheels do make for a smoother more comfortable ride.
I'm not convinced by those that recommend locking out the front suspension. One factor is when commuting you quite often carry loads, I have a toolbelt full of expensive engineering tools on my handlebars and usually a bag and laptop on the back, the front suspension is useful with these things. Commuting is a lot of different needs, speed isn't that big a factor for many people.
Worrying about pedaling effort is good if you're shaving seconds off a race I imagine, but in practice you don't notice it, it's like half filling your water bottle to reduce weight a fraction.