I agree that the rules might not be 'ideal' for the late mediaeval period - which I realise is something of a 'shoulder' period (along with Renaissance gaming too, I guess) where there a lot of features of both 'high' mediaeval warfare and that which characterised the 17th century - a mix of knights, archers, cannons and pikes.
Regarding the cannons, might you have a look at the suggested changes to cannon rules I posted somewhere else on the forum? I think that re-balances them a lot (i.e. makes their damage output relate to the number of ranks the target has, making them more effective against infantry in general).
I agree that another special rule to slow down other late mediaeval phalanxes (as you say, Flemish in particular, but Scottish too) might be in order - but that is a separate issue.
As I see it though, one should design lists with historical accuracy in mind firstly, then try and balance that as best you can against likely foes (i.e French and Burgundian ordonnance) mainly through points cost. Against these lists, the Swiss weaknesses are glaring - i.e limited cavalry, armour and support. They need something more than just the option to take huge numbers of pikemen and above average courage, as pikemen still lose against foot knights, and above average courage is only really needed when you are losing combat! Swiss need a little bit more, I think!
As I see it, having a slightly faster MR is historically tenable (indeed, it is well documented), and easy to implement. Other options to increase the de facto speed of the Swiss revolve around adding more special rules, such as drilled as standard (but that is less then perfect, as Swiss armies were also quite impetuous), or something new, such as a bonus to charge distance, or some mish-mash of drilled+impetuous. I just find the layering of special rules an unnecessarily cluttered approach. Similarly, the idea or open order pike blocks seems 'wrong'.
Now, I just think of profiles in relation to historically appropriate foes - i.e. HtH 3 is average, MR 10 is average. So, it doesn't matter whether a Burgundian foot knight or a Viking hirdman or a Roman legionary was the better fighter relative to each other, what matters is that he was better than the 'average' combatant of his day (a billman, a bondi, a Celt barbarian, whatever), and so he should have HtH 4. I reckon a Viking hirdman could probably march faster than either a Burgundian foot knight or perhaps a Roman legionary, but they all have MR10 as that is average for their time period. The number is only important relative to appropriate foes.
I don't know if that is clear, it makes sense in my head...
I haven't thought at all about the implications of taking my Swiss list out of context, and putting it up against (say) some Celtic barbarians or Archaemenid Persians - maybe they seem much stronger compared to them! We can all agree that the Swiss are said to have been very fast relative to other late mediaeval infantry. These mostly have MR10 in 'CoE Land'. Giving the Swiss MR12 makes them speedy relative to the infantry of any army they should fight, which to me is as it should be.
Anyway, I have rambled off quite a bit here. I would like to finish on a question. We all agree that Swiss armies had lots of solid combat infantry, were very brave, and were speedy, relative to their foes. These are their three big advantages. Their weaknesses have already been mentioned. Why is MR12/closed order so problematical when there are examples of the combination elsewhere, and it gives them a historically appropriate boost relative to the armies of their period?
I am sorry if this is too rambling/incoherent or otherwise bothersome. Anyway, many thanks once again for all the input, and I am curious to hear any and all suggestions.