Grr that's quite some observation you have got there hope it helps the developers,"|" is also confusing for me too maybe the developers could help here also like you said the size of updates could be reduced.
You don't need spybot if you have MBAM!
I definitely what MBAM Pro to go mainstream that just a addition.like said b4 it would great if MBAM Pro could detect and destroy hidden files,Autorun.inf,Autorun.in,ctfmon.exe,etc. folders in pen drives.One option which is difficult that could be considered is if some important file is infected,instead of deletion it should be cleaned[very few AV's do this],only when file is infected beyond cleaning it should be deleted.Site Advisor feature would be lovely.Detection of keyloggers is a must.Zero day protection could be given a thought.Smart updates which install fast without knowing is good instead of manual.Self protection of MBAM files from manipulation from other programs or malwares is again a must.