BillyS - 2:41 pm on Aug 30, 2013 (gmt 0)
I went through this upgrade in April too and my problems were minimal. You need to solve them in 2.5 because 3.5 will present the same challenges. Going into the conversion, I had a list of like 50 items I needed to check after the conversion. The below type of URI was on the list. I used SEF Advance, which automatically redirects the below to the SEF URL. Look around there are easy to institute solutions to this problem.
Of course Lucy is correct too. Once you're sure the server is going to return a 301 or 404 / 410 (whatever is appropriate), don't block access. Let Google know their redirected, bad or gone.