I replaced the QR skewers on the front wheel and seatpost with hex key units, and keep the tools in the bottom of the basket which clips to the front of the bike. I also have an ABUS Bordo folding lock which is nice and compact. When I stop for errends, I just lock the bike frame and grab the basket.
I never leave it outside overnight though, and my routine is such that the places I predictably go every day have secure parking so I don't even use the lock most of the time.
My goal is to make it as easy to use the bike as it would be a car. If I find myself thinking "yeah, I could take the bike but I'm worried about it being stolen" or it's a big hassle to lock or remove everything at each stop then I need a better system.
Ultimately, I'd like to have a GPS tracker like Boomerang. I'd prefer to do something to catch a thief, rather than simply redirect them to someone more vulnerable.
Also, have good insurance and a deductible low enough that if the bike gets stolen you are more excited about the prospect of a new bike than depressed at the money you've lost.