Can boiling a soup too low result in less flavor? I recently tried a new recipe which involved cooking vegetables at a lower temperature than I normally see. I had problems with the instructions from the start. The low setting on my stovetop didn't seem to do the trick to sweat the onions or simmer the soup until I turned it up to medium first.

As a result, I spent a lot of time waiting, and the soup spent less time at any kind of boil. The resulting soup doesn't have much flavor despite the ingredients all being fresh.

Could it be that the vegetables didn't get hot enough for long enough to do the job? How do I fix it?
I'd say that recipe really is going to depend on how much flavour is in your ingredients.

Nothing really has much time to 'cook' so the end result is going to be very 'summery' ie not far off 'just heated'.

You can't sweat down onions &amp; garlic in 6 minutes, but what you can do is just knock the raw edge off them.
Everything else gets about the same treatment, &amp; should come out almost al dente &amp; tasting really fresh.

The massive hit of basil &amp; parsley at the end ought to make it zing off the plate!

If it doesn't… then I'd look at your ingredient supplier.  

Supermarkets are great at selling you things that look fantastic, perfect in every way - except they can really lack flavour.
One of my pet hates is supermarket parsley [&amp; coriander/cilantro] It can often be nothing more than 'green', with very low flavour. Supermarket tomatoes, eggplant &amp; zucchini can be very similar.