If the storyline actually made sense then I wouldn't have had a problem with the location being on the east coast or west. Unfortunately, Wolverine's excursion to Magneto's base takes away the possibility of it being on the west coast near San Fransisco. There is no way Wolverine could have traveled all the way back to the X-mansion and then travel with the X-Men to San Fransisco in time to stop Magneto.
Why does Wolverine’s trip to Magneto’s base take away the possibility of it being on the west coast near SF? Why is there ‘no way’ Wolverine couldn’t have travelled back to the X-Mansion and then travelled with the X-Men to SF?
In the time taken for Wolverine to get back to the mansion (a few days?), Magneto and his army were somehow making their way from the forest to SF.
I don't have a problem with Magneto having a base on the east coast. What I do have a problem with Magneto's army showing up at San Fransisco a few scenes after Wolverine left Magneto's base. That's bad directing.
Why is a gap of a few scenes bad directing? The movie isn’t happening in real time.
There's no way Magneto could easily transport an army of that size across the country in such a short time period without our government noticing them. The Magneto of X1 and X2 would have found the least conspicuous way to take his army to the west. It would have taken more time but, at least it would have been more believable.
How do we know how he moved the army and how long it took? It must have been inconspicuous or the government would have tracked him. You say the Magneto of X1 and X2 would have taken more time but we don’t have time details, and we don’t know how Magneto moved the army and exactly how much time it took. An estimate would be several days, the time it took for Wolverine to ride back to the mansion (with breaks on such a long trip, if Magneto’s base was on the west coast) plus the short time taken for everyone at the mansion to prepare for a trip to Alcatraz. So, it must have been several days.
The methods he used to go San Fransisco in such a short time should have immediately alerted the authorities near Al-catraz. Witnessing how unprepared the military was for Magneto's attack on Al-Catraz was pretty far-fetched.
We don’t know the methods he used. He’d be clever enough to find some technology, or some mutant’s power, that enabled travel without alerting the authorities. Magneto obviously had the ability to travel without being intercepted - this information is provided to us at the start of the movie, when we are told that the government has had hits (sightings? terrorist events?) in Lisbon, Geneva and Montreal. Therefore travelling across distances without government intervention is already established as possible by some means of transport. Therefore, his travelling to SF is possible too.
And the military were not that unprepared - they had plastic needles in plastic weapons and took out the first wave of Magneto’s army.
Times, locations and distances were not shown... but they weren’t shown in the previous X-movies either. And the convenience of people arriving at certain locations at certain times has happened before as well in the X-movies. Those things aren’t problems, they are part and parcel of storytelling, especially where a movie’s length dictates that we don’t see every detail of every event. Sometimes, such conveniences will stand out as too obvious and contrived - to me, the Venom meteorite happening to land right by Peter in SM3 was too convenient, as was Sandman happening to stumble into an open-air testing pit. I didn’t see any conveniences in X3 of that nature.