C&C 3 is good, but I think its missing a few aspects especially after playing Supreme Commander. I completed the GDI missions in 2 days, after that there are the NOD missions, plus a couple extra.
On the other hand the missions in Supreme Commander appear to be long, I had one that lasted over 90mins. Which can be along time. I think there are 18 missions in total, 6 for each faction.
If you want replay value, both games have good skirmish and multiplayer modes.
I vote for Supreme Commander if you have the patience.