Obviously this was pulled from another site, so I don't want to steal all of it. Instead I'll post of a list of the questions posed, and then you'll have to read on to see why they were so important to the movie.
1) Why is Clu 2.0 evil?
2) Why do the programs hate Users now?
3) How could the ISOs be completely wiped out?
4) Why was the portal built so far away?
5) How did Tron return to the "Light Side"?
Of all the questions posed, I must say the last two were ones constantly on my mind as well were the last two.
The explanation for the portal leading to the outside world just didn't make sense. In one scene they say Clu 2.0 needed Flynn's ID Disc to get through it, but in another scene, they explain it was built up high so no program would accidentally walk into it.
I simply think Tron's re-conversion was poorly handled. It made some sense, but required a lot of suspension of disbelief. Interesting questions though, and they definitely expose certain holes in the plot. Holes I wanted filled....
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