Mathematical notation is ambiguous and therefore unsuited to parsing as a computer syntax. s(x + y) can represent scalar multiplication, or function application. Mathematica only uses s(x + y) for scalar multiplication and s[x + y] for function application to avoid this problem. Sin[alpha], etc. is just a symptom of its consistent naming convention for built-ins. The use of Capitalised names frees you to create your own function names in lowercase without fretting about namespace conflicts.

I've downloaded Mathics onto my Mac, unpacked it, installed it and tested it without issue. The web interface works well too. I'm very impressed with this software and appreciate all their efforts, especially what appear to be well commented sources. To complain that a better notation could have been used is to completely miss the point. This is for people who would like to use Mathematica syntax but can't afford the licence. I've got four books on Mathematica, but can't remotely afford to purchase it.