What is a bullnose corner? If it's where the base is rounded at the corners, I've seen shoemold installed on those. I've seen jobs with pre-made inside and outside corners on the shoemold. It wouldn't be too hard to make corners or you could have a millwork make them.
You might be able to wrap flexible shoemold around the corners and miter the ends to meet the wood shoemold on the longer runs. Something like this: http://www.amazon.com/gp/product/B006R98WTO/ref=ox_sc_act_title_1?ie=UTF8&psc=1&smid=A39EAJK4Y34QD0
I assume you're referring to gaps UNDER the base, not next to it. Scribing the base should fix these, especially if you only have 1/8" gaps. Scribing shouldn't make the base look wavy if done correctly.
It seems like your contractor is discouraging you from either method to remedy this problem. What does he suggest?

my contractor doesn't think it looks that bad. I disagree and don't want bugs and dirt collecting under there.

Even if you did close that gap it wont keep bugs or dirt from getting back in the walls.

Now closing the gap makes for a better look. And i agree with you that it looks tacky. Especially if its brand new. A good finish carpetner shouldnt even flinch when told to scribe base to a floor. Its almost second nature to them.

gregmills - our GC is the one installing the baseboards. He does do some carpentry but maybe he doesn't have enough experience with this? Should I try to hire someone else to do this?

So we should we scribe vs shoe molding?

jfcwood - our walls are rounded so yes that's what I mean by bullnose corner.

thanks so much for the responses!

my contractor doesn't think it looks that bad. I disagree and don't want bugs and dirt collecting under there.

There are pieces of molding made to match bullnose corners, or you can use multiple miters.