I've always been a $500 bike sort of guy but looking to upgrade to something with suspension.  It would be mostly for road miles but would like the option to off road without compressing my disks any more.  
The first shop I tried suggested a Transitions Smuggler mostly because he had one and the XXL model fit my frame.  Anyone have insight and or experience with this make & model?  Where else should I be looking in the $3k range?

Here in the PNW, Transition is a Very good bike for our MTB trails/conditions.  I'd be very happy with one and looked at them prior to my Santa Cruz

for mostly road riding its Very likely your overbiked, even with some light trails .. maybe looks for less suspension, more cross country oriented if you will want suspension, something around 120/100ish

Is there a down side to having that much suspension?  Other than paying for something I won't consistently be using?

Pedaling efficiency is what comes to my mind. The more squish it has the less efficient it is at transferring your pedaling to the ground. That combined with geometry could make it absolutely suck unless you’re riding some technical trails or bike park.

For "mostly road miles", it's at the max travel I'd consider. More travel, harder it is to peddle. 130/140 isn't too bad, the shock has a lever on it you can turn clockwise to make the rear shock firmer for road riding or going up hill. Single track dirt riding, 130/140 is great!

https://www.trailforks.com/  <<--- Top left, hover on Maps, click Discover by Map. Scroll to your local area.

Weight, efficiency, price to name a few.

There are a lot of "do it all" mountain bikes, but there are exactly 0 that are good the the majority of the time on asphalt and some mountain biking with full suspension. They're mutually exclusive, at least for now. If you're really set on the idea, buy an older XC bike that has a front and rear shock with lockout.

The Smuggler is built to be an all mountain bike, meaning going uphill, but also does ok going downhill in bigger terrain.