I can comment on Warren, and I'm pretty intimately familiar with those specific roads:
Going towards King George, I have never seen significant flooding. That stream is also just a stream (starts over near the center of town), it will not remain at a high water level for a long period of time post-storm like a river does. I believe there may be some points where it floods going the other way towards Vosseler, but again it's not common.
Snow kind of depends on your comfort. The main roads are usually cleared fine and going towards King George should be fine. The little backroads to your west/south will require you to know what you're doing (ex: Most people find
this road somewhat unnerving in good weather), but you have no need to actually be taking them.
Going down the hill towards 22, out of the main roads Mountain Ave/Morning Glory Rd usually stays open. Vosseler and Warrenville are usually closed.
Warren in general had significant power outages after the recent disasters. On the other hand, so did every other town in the area (and most of the state for that matter), and on the plus side I'm about 95% sure you are still in the PSEG service area rather than being on JCP&L (who has a much worse reputation for service restoration), as people I know a few streets over are on PSEG.
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As for traffic, most of the town is basically traffic free and I-78 usually is as well east of the I-287 split.
The one thing that will affect you on the way home, is that Warrenville Road/Mt Bethel Road will have a lengthy backup coming up to the turn for King George by the church/cementary, adding a couple minutes. If you are heading into the center of town after work for groceries or something, there will be another backup coming down into the town center.
There's nothing else in town that's worth noting for traffic problems, and you have a lot of alternate routes since there's a lot of side roads with 35-40mph speed limits.
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Schools are good. Schools are also good in Basking Ridge. I would not make this a significant factor in your choice, the differences are minor.
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They're both great towns which are doing well. Being next to a quarry and a train line isn't great for resale value, on the other hand it's already factored into your purchase price (and the train line is electric with no freight trains, which helps), so I doubt the BR house will track differently than the rest of the town does going forward.