First off, you're on the right track that startup time in the polyfilled environment is a hotspot. But this is an area of extremely active development - especially the shadow DOM polyfill, as we work on trying to minimize this hotspot in the short-term. It's more of a concern on mobile, which may or may not be relevant to your environment. We should have more news to share on this shortly.
One note of caution - generally when profiling, it's pretty easy to fall into the trap of micro benchmarks. Certain DOM operations can be significantly slower in the polyfills when tested in isolation, but much less so in real world scenarios.
We'd be happy to take a look at whatever you find, or scenarios you've found to be particularly problematic.