So the main problem I have with the new version is that if I happen to download a file that I already have with the same name in a folder. Opera 28 now decides to add (1) at the end of the file name causing me to have duplicate files which is very god damn annoying.

Don't you get a dialogue how to save? There must be one.
Besides, while in practice those are more often the same/'duplicates', in principle they do not have to be such at all. Apart from occasionally the same file-name url part for a couple of files from different pages/servers, the files' contents themselves are not written in stone and subject to a possible or scheduled change on the server side (of course). It might relate to graphs, images on weather forecast/observation services, for example. Or when it's user uploaded content, it might be subject to updates by the users.

I say what? You can just backspace those parenthenumbers in your download dialogue. For the dialogue to appear, you might need to check certain settings in the browser.