A Second Story is a neat idea that could eliminate wiring with a suitable case that can take advantage of PCB mounted connectors.
Here's my wish list...
1) Well the top of my list is a really effective AGC. This is what separates a really great rig from a really good rig.
The basic MicroBITX so reminds me of my SBE SB-33 (1966 - mobile rig) it is the audio derived AGC.
Back in the day Collins S-Line had great (but complex) AGC that worked(s) great, but..
Nearly every Heathkit SSB rig back in the day had great AGC whether it was a tube HW-12 or a solid state HW-104.
Check out the HW-104 AGC system...
2) Solid CW Keying and for a paddle
3) USB interface to rear panel - One big reason for this kit is to become proficient working with software.
4) Well if those are done an S-Meter is nice.
Nice to have:
4) Momentary button to toggle between VFO A and VFO B. If you work split this is really necessary (Yes, I chase DX on QRP)
5) Mic Pre-Amp and Mic Gain - I added this tonight with the PCB temporarily stuck on the rear panel (all my jacks are on the rear panel out of the way of knobs.
It helps a little so I don't feel like I have to climb in the Mic, however a Speech Compressor might be more worthwhile. Being able to use typical Electret Condenser Mics (e.g. ICOM radios) it needs more gain and an adjustment even if a PCB mounted internally accessible set and forget pot.
6) Keying interface for a Linear. Band data and keying - This baby will drive an RF-KIT 2K+ LDMOS linear to legal limit. (when life is too short for QRP)
When you have nothing better to do:
7) VSWR Bridge with Display for forward/reflected power. The tuner gets a lot simpler and an external tuner may not need power (manual tuner).
Oh, wait, didn't you do that one already? LOL