Most of that stuff is really up to the programmer and not due to the tool. While i agree that VB6 wasn't a good tool to write big projects on, it wasn't because of the issues you mentioned (since those would apply to something like Delphi and Lazarus too and they are certainly fine for making large projects on), it was because at its core it was a rather simple and limited scripting language bolted on a WYSIWYG form designer with some database stuff latched on via an extension system.

If anything some aren't even issues but features - e.g. being able to have code attached directly to events speeds up development a lot and if you need to put it somewhere else (IME the case where this isn't necessary is more common than the case where it is) you can simply have your handler call some method in another file so you can keep those separate.