After some messing around and with nice advices of Gulliver I found out that 3.5 isn't faster if you disable some WBStartup applications that for some people (incl. me) aren't so important from 3.9:
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AmiDock (extra toolbar for application, that is kinda heavy shiz)
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AsyncWB (for better asynchronous file operations - if you copy or delete multiple files at the same time)
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BenchTrash (Global Trashcan, like the recycle bin on windows)
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DefIcons (for configuring easily, custom actions by default, on a set of specific type of files)
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RawWBInfo (for more complete Icon information windows - basically arranging stuff in 2 tabs)
You can also use Env-handler that saves precious Chip RAM by holding environment variables in a more accessible fashion.
Also 3.5 has memory leaks AFAIK so I'd suggest using 3.9
