I think the whole "user power" thing tends to be overstated. Sam had no particular special powers (other than bleeding) that we ever saw. The powers Kevin Flynn displayed in
can be explained in terms of his intimate knowledge of the system gained by being a hotshot programmer in the "real world", not to mention directing the evolution of the system in Legacy
plus thousands of cycles during which to practice.
If a data entry operator or other low-skilled user, in terms of programming and system administration, had been digitized instead of Flynn, it's unclear at best whether that user would have displayed "user powers".
I agree with Kat that CLU certainly had high level privileges - it would be necessary for a system administration program - and these would manifest in ways that might resemble "super normal" abilities. (The whole question of "normal" is up in the air, though, when we talk about the Grid. The rules aren't written down somewhere for us, the viewers, so we're left to guess and ponder.)
As for changing colors, it would have been interesting to see what happened when programs "renounce[d] this hysterical belief in the Users" and became soldiers of the MCP. Did their circuits spontaneously change colors? Did they have to visit the MCP's mesa for conversion, something like rectification? Hmm...