I too, think that we should be honest with catechumens. I teach the catechumen class at our parish, and when I discuss certain issues (like the issue of jurisdictions, or language, or pews, or organs/choirs, or women in the church, or headcoverings/dress, etc.), I am quite upfront with them about the fact that these are areas where the Church needs improvement, where individual parishes (even when it's a lot of individual parishes, or most individual parishes) need to make some changes. I tell them gently but clearly what I believe, what the Church teaches (with the assistance of the priests, catechism materials, etc., of course), and what is actually happening in the parishes. Sometimes they are, indeed, disappointed, confused, and even upset.
But I make a very clear distinction, which I think is important for all of us to remember... while the Church is perfect, the people who run it and the people who are members of it are NOT. And there is always growing to be done in our journey to theosis, both as individuals and as a body worshipping together. And I try to offer them the opportunity to be part of the solution, by suggesting that they talk to the priests, write to or talk to the Bishops (if they feel very strongly and want to), write articles (like the famous "12 things I wish I knew" by Fredrica Matthewes-Green), etc. And of course, I tell them to seek guidance in grappling with these issues from a spiritual father, and pray about them. I find this is the best way to approach it. Honesty and love, admitting our downfalls and trying to improve upon them, being part of the solution rather than allowing the problem to continue.