Appearance:
A.1) individual color assignments per transaction in the registers (no I don't want to change the entire color scheme, I just want to "mark" a transaction so it is easy to find later in a session, or across sessions.
A.22) Ability to put a variable width/variable color blank bar as a dummy transaction/separator, perhaps indicating end of period, or a place where I want to come back to later, I currently use a zero-amount transaction for this purpose, and mark it "reconciling" and have a slush/reconciling account as the other side, but a simple marker would be more attractive. and easier to find. Note that implementing #A.1 above would obviate the need for this feature.

Function:
F.1) Ability to mark one or more transactions in a register as "ignore this item" - useful for quick eyeball reconciliation without having to do a "formal" rec.
F.2) better templating of splits, e.g. for a paycheck where earnings, taxes, etc. can change, but insurance, etc. deductions don't, and 401K contributions are formulaic
F.3) Ability to work as of a "fake date," show registers and totals as if you are working as of an arbitrary date. This would make it much more convenient to correlate paper statements (which are sometimes received months late) with register entries, and the accounts/categories that they effect. Yes, I know that one can show a range of dates in the register, but this does not affect the summations.