Shakers RULE!!! 99% of the time, this is what I use. Done in 2 minutes. The thing I like the most is the easy clean-up. This time conservation is handy on a tight schedule during school periods...and late at night when everyone is asleep and I am tired. If a protein is bad at mixing, you will need to change brands as this is a sign that the protein may have been denatured. It doesn't mean that it will not be digested, although not as well (all of it will be digested), but it will make it a pain in the ass to mix as you have stated. There are other things which will factor in such as its lipophilic and amphoteric properties, which means that it may or may not be better mixed with fats or water better.
BMJ