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I think the oven method is SO much better and really doesn't take much longer at all. The only time we have microwaved nachos is when just one person is making a few for themselves and we don't want to heat up the oven (and kitchen) for just one person.
We tend to make nachos with tortilla chips (usually store bought, occasionally I make my own), canned refried beans (fat free), and grated sharp cheddar. Then, after they are out of the oven top with a bit of sour cream, jalapeno slices, maybe some homemade salsa. Salsa is so easy to make in the food processor that I cannot fathom ever going back to the jar stuff again, or even the deli stuff we get here at the grocery store (because it is good but so expensive!).
I don't personally notice the taste difference between buying whole pintos then smashing them over buying canned refried beans. Neither is going to taste as good as refried beans from scratch but I don't think they taste "bad" out of the can, at least not once you add stuff.
For chicken nachos, we use shredded chicken, preferably grilled with citrus flavors, and usually skip the beans or use black beans instead. For some reason the two flavors taste better to me (chicken and black bean) -- and with chicken nachos I always add sour cream, sharp cheddar, a squirt of fresh lime, as well as some cilantro.