This is an interesting issue actually. You see, your v3.6 actually issued the SIZE command behind the scenes before starting each transfer. That's why you don't see 100 instant [size equal] type messages for 2 identical dirs, but they instead show up slowly. The server has to send and wait for a reply for each file individually. Using advanced settings you could disable that in that past (not sure if possible in v4) but it's actually a good thing most of the time and well worth keeping enabled... The question I'd pose is should you SEE that or should it be hidden in the status window. As an FTP server author I want to see everything the client is doing, but I can totally understand (and often want) to not have that spam cluttering things up. An option to hide that query/response sounds like a good thing to me!
The MDTM check is a bit more subtle. I like your suggestion of making it optional, plus another option to hide the spam if enabled! If you don't enable it however adjusting the timestamps on local files is a bit trickier to get right. I think using the timetamp from the directory listing would work well (after using one MDTM to determine any offset being applied) and would speed things up. Allowing you to choose speed over accuracy for a particular site might be useful. I also haven't tested this, but I assume that if you disable the "preserve file date" for the type of transfer you are doing and don't have any time based file transfer rules it won't bother requesting the time via MDTM at all. Even then it could use the directory listing to weed out obvious matches for timestamp comparisons and only request it if tricky to determine...
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