MongoDB: Index intersection does not eliminate the need for creating compound indexes
There are a couple of reasons for this at present (I say at present, because improvements may be introduced in the future that reduce the relevance of these points):


Index intersection is limited to 2 indexes (this was the case in 2.6 but I don't see anything in subsequent release notes to suggest this has been increased)
If you can predict your query patterns and cover them with compound indexes then this will likely perform better
Index intersection is currently essentially a last resort to provide some index based coverage (as opposed to a table scan for example) for query patterns that are not already covered by a more efficient method


This is true for most purposes and most query profiles. A counter example here would be a set of queries, regularly run, which would require a large number of compound indexes. The work being done to keep those indexes up to date, the amount of memory they take up might mean that index intersection is a better strategy. This, however, is an edge case - most database usage can be profiled and indexed efficiently so that index intersection is not required.