Why exactly is Process.Start() not working for you? In the absence of that knowledge, I can only describe the situation I encountered when trying to kick off the .NET installer.
If a UAC dialog is appearing, requesting admin privileges, there is no way to avoid requiring your user to click it. Any non-elevated installation process, including a professional third-party solution, will encounter the UAC dialog when attempting to start the .NET installer. This is because the .NET installer requires an elevated administrator token to run. You can't get around that.
Dealing with a background UAC dialog was what I encountered. It would blink silently and be overlooked by users who probably thought the installer had frozen and gave up on it entirely. I just spent 2 weeks working on this issue. It only happened if the user clicked outside the installer window between the installer starting and the UAC dialog appearing. Doing so makes Windows think the user wants to work on something else, and keeps the window he clicked on active. Windows is designed to inhibit "focus stealing", so there aren't any official ways of "grabbing" focus back for your window (i.e. for the UAC dialog your process started).
It's safe to assume that the window your users click on aren't owned by you, so the official Windows methods (having the window with focus grant permission to your process to grab focus) won't work for this situation. This is where it would be nice if msiexec.exe had the ability to keep its windows top-level.
So at this point, if you are encountering what I encountered, then there aren't any simple and Microsoft supported solutions to it of which I am aware.
But perhaps you are running into something else? Again, please update your question with more details so we can give you a better answer.
Changing installation IDEs, as another user suggested, no matter how good the target IDE, is a big step. And as much as I cannot recommend using Visual Studio to develop MSI files, I would consider moving to another IDE only if you should continue encountering problems doing what you want to accomplish. So far however you have described only a localized problem to resolve, and one that may not be resolved by using another tool.
