The first comma is simply incorrect. "unfortunately" does need commas around it, but it could be moved to the beginning for a simpler sentence.

The fourth comma is also incorrect and should be replaced by a semicolon.

"Unfortunately, the problem is that sometimes these tools are just not sufficient; it's still easy to shoot your own foot and get lost in a sea of complexity."

And looking at that now, I would also get rid of "the problem is that". "Unfortunately" and "sometimes" back to back lacks flow, so I would also replace "sometimes" (in this case with "often" in place of "just"). In the original, "just not" has a stronger grouping than "not sufficient", which is why "insufficient" wasn't used. Now with "just" gone, I'd swap back in "insufficient".

"Unfortunately, these tools are often insufficient; it's still easy to shoot your own foot and get lost in a sea of complexity."