Hi Majo,
I’ve currently no access to my MIDI gear, but I remember this imperfection. Sorry, I forgot to fix this in V1.6 - however, so far I know it can only happen if the CC target of velocity/aftertouch/modulation wheel is assigned to its own init value (velocity: CC#2). I will try to prevent this combination in the next release.
All the other CC targets should work.
You don’t need to upload MIOS and the application again if you’ve assigned this critical CC by fault, you only have to prevent that any note will be sent to the SID until the CC target has been changed to != CC#2
Change of Link button: for some people thats a very important button if they are working with an inflexible sequencer like Cubase which doesn’t allow to reconfigure the MIDI environment on-the-fly to avoid feedback loops during startup or if CC data is recorded. I’ve implemented this function on request by other people, and don’t want to remove it again.
Superpolyphony: is definitely planned - see also the StepB introduction page
additional play modes like Super-Poly, Super-Arpeggiator, Split, Layer, Unisono are possible and planned for future extensions.
Superpatches: up to 16 combinations are prepared (saved at BankStick address 0x0080-0x00ff), but I haven’t found the time to finish this yet (I’m working on other mighty applications like MIDIbox SEQ in parallel and prefer to play with the new possibilities by myself before implementing the next ones, therefore it can mostly take a long time before such ideas are available… - please understand this)
Joining outputs: without the resistors you would have a short circuit. However, I recomment the use of 4 seperate audio inputs of a soundcard (so that effects can be routed easier in the sequencer software), or the use of an external mixer.
Routing Velocity/Aftertouch/Modulation to more than one CC: unfortunately not possible anymore since the patch structure is frozen — and especially heavily overloaded since I’ve already implemented so much features
See also sid_sysex_table.inc - there is only one byte free anymore in the patch.
I would have to cancel other features to realize this.
Modulation matrix with different depths: two years ago I decided to implement the sound engine different from traditional synths. Common synthesizers have only one or two LFOs, one envelope generator, and a modulation matrix which allows to route these signals to different targets at the same time.
But I found it better to have more LFOs and EGs which can only be switched on/off to the targets. Advantages: more expressive sounds, easier and less complicated handling (especially nice for live playing), cheap control surface (only 56 buttons and LEDs).
Since the depth can be controlled at the LFO/EG directly, I didn’t find a reason why I should add 56 additional depth parameters (which would consume 21% of the patch structure) for the targets.
Of course, people think “Synth A and B can do this, why isn’t it implemented in MIDIbox SID”. My argument: because it’s different and has it’s own charisma and especially some features which cannot be found in other synths 
If you want to have another concept, you will have to reprogram the whole application at many placed — and not only this — you would also have to change the whole infrastructure (new control surface, new editor, overworked patches, etc…)
Hint: if you want to realize really expressive sounds, then use the wavetable sequencer for (up to three) additional modulation sources. Imagine that the sequencer can modulate the modulation parameters of LFOs/EGs, but also his own input parameters.. Oh, I just have noticed that such a possibility is also not given in other synth architectures, therefore maybe unknown by most of you guys 
Best Regards, Thorsten.