I like the Homeworld refernce, great game.
You are completely right about the massive time to complete and resources needed but I pretty much assume we were treating these(collective ST/SW/Other) as pre-built. Also when you control an entire galaxy resource amounts and costs are a non-issue.
What happens to communication in the "Star Trek Universe" when the home worlds of each faction are destroyed? I'm pretty sure the Federation would have a communications break down if the people of Earth all cried out at once and were suddenly silenced.

Of the ST factions I give the Borg/Species 8472 the best shot.
Keep in mind that SW took place "a long time ago, in a galaxy far far away" and ST is based on our reality and won't happen for another 3-400 years. Assuming that the SW galaxy didn't collapse and all sense of innovation was not lost they've had plenty of time to improve the tech.
That said, afaik, neither fiction has figured out a way to leave their respective galaxy so the whole issue is pretty much moot. I enjoy both ST and SW equally but for difference reasons. I like the logical attitude of ST and I enjoy SW for the whimsical, "lets think of the coolest sh*t thats not remotely possible and lets do it" stuff.
Oh, and HAN SHOT FIRST!
IIRC, V'Ger's cloud was AUs in diameter. That's MULTIPLES of the distance from the Earth to the Sun.
Anything capable of generating that much power makes whatever powers the Death Stars look like a match in comparison.
Don't forget the whale probe was able to shut down electronic devices simply by being in proximity to them, and is able to vaporize oceans by transmitting an audio signal.
Uh if you want to get technical about it, the cannon is 2 AUs, thats the diameter of the earths orbit. V'ger was putting out power "greater than 1000 starships". The power output of the Enterprise D is stated as being 12.75 billion Gigawatts. I'm going to assume that the Enterprise D is more powerful than any ship in the Federation at the time of the V'ger encounter. The Death Star II generator was equal to the output of seven stars main-sequence stars. Our sun happens to fall into that catagory. Its assumed power output is 386 billion billion Megawatts. Now I suck at math but I'm pretty sure that the Death Star would have a higher theoretical output than 1000 V'gers.
And the whale probe? It vaporized water with an energy wave. I can do that in the microwave. The Death Star vaporized an entire planet.
Like many have said, the SW universe is blown so far out of reality that ST flat out can't win simply because it tries to stick with known rules. Honestly Q could wipe everything out but I think he'd have to much fun watching the battle unfold.