Many of the issues you have mentioned have been requested or discussed in this forum previously. I would also like functionality in Custom Reports to be able to select General Ledger Balances in addition to the existing General Ledger Transactions.
In the meantime I have found that adding a unique inconspicuous character to the Account names in the Chart of Accounts for the accounts you require in a particular report is the easiest workaround. For example if you want a report with only Current Assets and Current Liabilities add a dot (Full stop/Period) on the end of these account names.