I find Ada is about as aggressive as your flesh and blood companions. A normal, scratch built bot, seems to be more aggressive, which is not always a good thing (Hence my earlier suggestion to boost Chr. up to 8 and get 1 rank of Influential, to keep your bot from nuking you along with the enemy).
Robobrain tracks are the way to go, hands down. Faster than 2 legs, more mobile than 4. Add on a sentry torso with mortars (or nukes if you're feeling lucky (punk)) and either a robobrain head (for the mesmer attack) or the Assultron laser head. An explosive gatling laser and the stealth blade for arm weapons and a tesla coil torso mod...throw on the armor that deals poison damage and your good to go every time.
As for supply routes, I tend to pick the shortest route available. So I have a line from Starlight to the Boathouse, or Starlight to Greygarden, to Oberland, to Hangman's Alley. The longer the route, the more chances there are for things to get mucked up. On a side note, yesterday I surprised a gang of Rust Devils as they started to attack one of my supply bots. Two-shot Gauss Rifle to the face for everybody!