I really loved Legacy, but I agree the bit at the end about invading the real world was completely unnecessary and straining "credibility".
I wouldn't be surprised if there was a more specific plan for Clu worked out, but much of it didn't make it into clear dialog in the shooting script.
To be fair, the very BASIC logic laid out by Flynn should have scary implications for anyone: "Clu figures if I can be in here, he can be out there". There's a few things implicit in that statement.
Assuming Clu can in fact take Flynn's place, that alone is a clear and present danger. Clu is as smart as Flynn, who is something of a genius. He looks like Kevin Flynn. Sounds like him. There's a real danger he could find a way to take over Kevin's old company, which in Tron is now one of the richest companies on Earth. Clu is also a misguided megalomaniac. That's enough "game over man" for anyone. Bad things would clearly result.
Honestly, the only unfortunately unclear thing we see on the screen is that Clu isn't just trying to get Flynn's disc so he can "open the lock" from the inside and beam out himself. He's flying a carrier to the lock, and plugs the disc into the carrier to program it in some way, for some plan. And Flynn says "he's found out a way to take it all with him".
In the overarching plot for the series, which as evidently already been largely mapped out before and after Legacy, that could have been referring to Clu escaping and transferring his own forces, electronically, to the computers of the outside world. As just one scenario.
As for places a Tron 3 could go, in fact there's a lot of possibilities that flow naturally from the end of Legacy. Look at it this way. Sam Flynn has just been handed the keys to a powerful megacorporation. He is now beyond rich. He has discovered an alternate dimension. He has a device that allows people to enter, and entities created inside to be extracted. He has renewed drive in life thanks to discovering the fate of his father.
Clearly, this boy is going to start some sh*t.
Plus, don't forget - Ed Dillinger Jr, and Dillinger Systems, Encom's rival in the technology world.
My own guess is that full of perhaps naive idealism, Sam will attempt to continue his father's work as well as reforming Encom to support Flynn's vision of technology improving life in the real world and spreading information enlightenment. And probably overreach himself (like father, like son), with some critical miscalculation, and the story is rolling. Very likely, the situation may be taken advantage of by Dillinger Jr.