Scramble bombers sucks because it will only give you a couple additional bombers. Picture late game when you have 20 transporters. You really want to spend antimatter to have a couple extra bombers? The other thing is, it competes with repair cloud for antimatter. This is why I choose microphasing aura every time I have to choose something beside repair cloud - it doesn't use any antimatter.
Like others, I also believe that Scramble Bombers is a better early game choice (rather than repair cloud). From my observations, Scramble Bombers is also what most of the 'pros' pick first. By my calculations, the 3 extra bombers for 2 minutes, can deal considerable damage, which by comparison to other level 1 abilities, is one of the highest damage abilities available. Granted, the presense of fighters can potentially severely reduce the effectiveness of Scramble Bombers. So maybe pick Scramble Bombers first, then Microphasing Aura, to help level up your Skirantra to get Repair Cloud for when you have a larger fleet, and its repair of ALL ships/strikecraft within range is more significant. The 200 hull point repair of a single ship for 100 antimatter is not that good. A definite antimatter hog. Thus, using the Skirantra differently might also help your performance. IDK.