I have a few:
-GNR's Supply Line:
Assist four Lyons' Brotherhood of Steel Knights in taking all six supermutant strongholds (I think strongholds placed along paths throughout D.C. would've made supermutants less abundant but as much of a threat) that are along the road from the Citidale to GNR to have both locations strong due to support from one another.
-Road to Rivet City:
Assists six Lyons' Brotherhood of Steel Knights in taking all eight supermutants strongholds on the road from the Citidale south to Rivet City. This will spread Brotherhood influence to Rivet City and increase reputation with both of them (if there had been a reputation system).
-The Taking of D.C.: (Only after the first two are complete)
Eliminate the last three supermutant strongholds in the Mall (they are much bigger than the others) to ensure safety for all of the Capital Wasteland.
-Dealing with the Outcasts: (Only after the first three are complete)
One of the supermutant strongholds in the Mall was a military bunker that had a dozen gatling lasers and plasma rifles; now Lyons thinks the Brotherhood has the man power, fire power, and time to take on the Outcasts but wants you to take care of it. Choose to either leave the eight knights (who also worked for you during the other quests) at a distance from the Outcasts' base to negotiate with them or just lead a full on attack. If you negotiate there four possibilities. One is that you persuade them (with a speech skill of 75 and/or reputation with the Outcasts) to rejoin Lyons. Another is that you convince them that Lyons can and will wipe them out unless they are useful and willing to join the Brotherhood (requires speech at 50 and three of four other skills at 75 (repair, energy weapons, big guns, or sneak)). If you teach them sneak and any of the other three options then they become their one squdron in the Brotherhood, sent on stealth missions whenever needed. You can also (with a speech of 50) convince them to become allies with Lyons, but not a part of them. The last option is if you fail every speech check and cause an all out war between the Outcasts and Lyons.
-(option in) Big Trouble in Big Town: (once all of the above quests are complete)
An option to get four Brotherhood of Steel knights to move to Big Town to attack the Germantown Police HQ and then protect Big Town. This spreads the Brotherhood's influence to Big Town and gives them a foothold in the north.
-Evergreen Invasion: (happens a week after Dealing with the Outcasts is complete)
Raiders from Evergreen Mills take over all of Springvale and are planning to invade Megaton. If you are liked or higher by Lyons Brotherhood than you can convince them to send a dozen knights to defeat the raiders and station themselves in Springvale. If this happens then you need a speech check of 65 to convince Lucas Simms that it is for the best, if you fail it then Megaton will grow more and more hostile with the Brotherhood over the coming years.
Now post what you think would've improved F3, this is what I think.