The Send a Message tool only sends to the "individual email" address. This way sensitive communications (such as to a bishop) can remain confidential. My wife is Stake Primary President and I do not receive any stake council communications sent to her individual email address, which is as it should be. It has nothing to do with being unequal. Your wife should make sure her email is listed as the "individual email" on her membership record - if that is blank, then no one will be able to email her using the tool and that would be the reason she is not receiving anything.
To request a change to the church software, you can send feedback from any church page and detail the request along with reasoning explaining why the current situation is not working. You can also ask your Stake President to bring it up in the coordinating council he participates in if he feels it is important enough to raise it with his general authority. The church service missionaries who monitor those requests can forward it to whomever makes decisions in those matters.
Also, the problem may be that whomever is sending the communications neglects to add your wife to the distribution list. For me and my wife, general communications from church headquarters come to both of us in our individual email addresses so you might be referring to local communications. Those leaders have the option of pulling up a list of all sisters, all brethren, all parents of youth, etc. and they may be missing your wife due to oversight and not any desire to be disrespectful. If this is the case, I recommend you have a discussion to them and ask them to include your wife on the communications you are referring to.