I only have two complaints about Moneydance and I think one of them is because I've been too lazy to figure it out.
The first one is that I always forecasted account balance in my primary checking account to make sure there's enough money in the account. With Moneydance, it seems to take into account the reminders, but not future dated entries already in the account. This is the one that I think I might be doing something wrong.
Maybe I can help with this one.
On the home page, look at the header over your bank accounts (the one that says "Bank Accounts". Just to the right of that is a changeable item that can be Current Balance (as of right now), Balance (as of the most future entry), or Cleared Balance (self-explanatory). The default, I believe, is Current Balance, but if you change it to Balance, you will see what you're looking for. I may have misinterpreted the question, but this might help.
The other one is the portfolio reports. In Quicken (and MS Money before that), I was able to display my portfolio based on the investment, not account.
I have to agree with you on this one. A number of people (including me) have asked for exactly this feature, but the developers haven't implemented it yet. I maintain my own external spreadsheet to handle this issue.