The final SG1 movie was suppose to take place/release before SGU was a thing, and yesthey were going to publicly disclose the program to the public. SGU would have either dealt with that differently or taken place before it.
The whole Eli thing in SGU was essentially going to have tied into that Stargate MMO that never happened either. Really as a franchise Stargate imploded rather spectacularly, which is a shame (especially since some of it was just MGM stupidity rather than the fault of the shows), but maybe it was better to leave it where it is.
Either way if they reboot it you've still got at least 8 or 9 solid seasons worth of good episodes to enjoy from all the series.