Ya I guess that could be an issue, we do almost all our designs with active x-overs so it would be less of an issue for use to do EQ. Where is the response issue is is high or low?
I've not measured it on a 2Pi baffle so some of what I'm seeing are baffle effects. It peaks around 1.2K but that will change based upon the baffle you use. In the Kepler you get the dual issue of the baffle diffraction AND the surround resonance to deal with so its a double whammy. With a DSP it should be easy as pie to deal with but you still need to measure it on the baffle to see exactly what your dealing with.
Once its dealt with in the crossover its a non-issue but doing so takes some extra work.
What do you consider low? I'm using 1600Hz 4th order acoustic in the Kepler and that works pretty good for both the tweeter & woofer.
Are you sure you have 100W per driver? What kind of signal are you using? Use a stepped sine wave starting around 20Hz and you should see a lot more excursion than that with that much power, especially in free air.