To be honest, VB .Net, based on .Net Framework, has better Windows integration, and more importantly, easy access to Windows core functions (I think you may need this a lot). For example, registry accessing requires quite a few API calls, and you need to take care of things more than just calling those functions. But in VB .Net, it's been wrapped as Classes and things are a lot easier.
Still there are some disadvantages indeed, for example:
1. VB 6 and VB .Net is very different (I bet, more different than most of you think) when it comes to system-related programming. Re-learn
2. If you prepare to distribute your program, your users have to have .net redistributable package installed - that is not a small file. Usually a user wouldn't want to download a file 20MB+ large, for a small tool.