The NCR don't need to capture Flagstaff to win the war. If Caesar dies and the legion fractures, that suits them just fine. The Allies never captured Berlin in WW1. And the more the legion get pushed back, and the longer the NCR hold the Mojave, the harder it gets for the Legion. If the NCR entrench and consolidate, it gets harder for the Legion to cross with every attempt. And if the legion wastes all its resources on Hoover Dam it leaves itself open to internal revolt and external forces. There's 200km of desert with the Sierra Nevada protecting the northern flank. Even getting past the Mojave Outpost would be a nightmare for the Legion. Getting up that hill if the NCR set up artillery and machine gun emplacements? They'd lose thousands. And as Ben Soto has said, the closer the Legion get to the Core Region, the better the NCR's infrastructure. They've got railways to move troops and supplies in the West. The legion are using brahmin. The Brotherhood are a spent force. It would be suicide for them to attack the NCR, and they know it. And besides, if the legion control the Mojave, they would probably fill the bunker with concrete and drown anyone inside. Caesar is pretty explicit in his desire to see the Brotherhood gone. We know nothing about the tribals in California now. It's a bit of a stretch to say Caesar would find it easy to assimilate them. It's not like the Dead Horses and the Sorrows have jumped at the chance of joining. But first they have to get to Shady Sands. I suppose Caesar could go full Hannibal Crossing the Alps on the Sierra Nevada, but it wouldn't take a large force to cause massive losses to Caesar in the difficult terrain. And moving the bulk of his army through the mountains would leave Caesar open to a counter-attack by the NCR on his own supply lines while he's bogged down in the mountains. We don't know about the Shi. They're not even mentioned in New Vegas, which suggests to me they no longer exist (as if they were still around, they'd merit a mention at least). I reckon absorbed into the NCR. In any case, they're intelligent folk. They're not going to be stupid enough to side with Caesar. Either they don't know him, and they're too clever to side with a complete unknown, or they do know about him, and know about his treachery towards past allies, probably including the Khans at this point.