As someone else already posted, check out
www.dogfoodanalysis.com
Not all foods will work for all dogs, even with high quality foods. You may need to experiment over time to see what works for your little one.
Unfortunately, most vets have very little training in nutrition so I would take any veterinarian's opinion on food with a grain of salt. Purina ProPlan, Science Diet, Iams, Eukanuba, etc are all very low quality foods.
Your puppy probably had loose stool from transitioning to the new food too quickly. I have Maltese and transition foods over a 2-3 week period. Another possibility is that the new food is too high in protein for your puppy. You may need to start with something with a moderate protein level.
My favorite moderate protein level food is Acana grain-free. You definitely want to purchase a grain-free food, whichever brand you end up with. If you think your puppy has a sensitive digestive system, one food that is good is Natural Balance LID. It is not "the best" food for a perfectly healthy dog because the ingredients are so limited, but it is a great choice for a dog with special needs. Someone else mentioned Wellness...that is also a good option, as is Taste of the Wild, Now! Grain-Free, and Orijen (though higher in protein).
Make sure whichever brand you select states that it is an "All Life Stages" food, or is a puppy formula that is grain-free. All life stages means it is nutritionally sound for both puppies and adults.
I also use the Whole Dog Journal approved food brand list which costs money to subscribe to, but the 2011 list is floating around there somewhere so if you do a google search you can probably find the approved list.

It is useful in finding brands that are high quality.