I have learnt so much about basses and Alembics in particular in my 10 years of ownership and assuming I was ordering the same instruments I already have but as new builds.
For my SC Signature, I would have Anniversary electronics with additional master volume and 3 position q-switches, slightly slimmer neck profile and standard frets below the 12th fret and smaller frets above the 12th fret. I'd try out a vermillion core with two thick maple body laminates like PierreYves and keep the cocobolo top and back.
For the Bocate Europa 5 I would have a cocobolo top instead of the bocate and Elan headstock, again anniversary electronics with additional master volume and 3 pos Q-switches
For the Black Europa/Elan, I would have a standard neck width rather than the narrow one I have at the moment, I would stick with mainly maple construction but have African blackwood top and back, blackwood on the headstock front only, signature electronics with 3 position q-switches, alembic logo and name on the headstock. Possibly all black hardware too.
Purple Elan 4, I'd just have a narrower neck profile and signature electronics, with clear finish to show off the body woods. I'd keep the P-style pickups but find a better way of securing them rather than the allen screws which keep unscrewing.
Series II 5 I would just have an Elan headstock, and alembic name inlaid under the logo and the logo backlit when used with the DS-5
For all basses I would have the Europa's bass and treble boost and cut switches as they are fantastic for quick mood/tone changes in a live situation. If possible I'd like a trim pot inside the control cavity so that I can choose the frequency that the bass switch operates on as whenever I use it I feel that the boost needs to be at a lower frequency. Also the ability to use the Series cable to power the basses via the DS-5.
For the series I guitar. I'd stick with the same body woods but on a a spectrum body, three pickups, 5 position blade switch, filters & 3 position q on all pickups, no individual pickup volumes just an overall master volume.
That's about it.