The issue at stake is the way by which lightning initiates. Observed electric field intensities in thunderstorms are several times smaller than required for dielectric breakdown (the point at which electrons and other particles are accelerated in the presence of the very strong electric field to the point that electrons flood from a source to a sink). In other words, the E-field intensities that have been observed by numerous balloon launches, rockets, and aircraft observations through storms have never been strong enough to cause breakdown in dry or moist air. While the breakdown field strengths are ~3000 kV/m and 1000 kV/m for dry and moist air, respectively, the majority of observations have shown peak electric field intensities of 300-400 kV/m (though some have been closer to 700 kV/m). Corona discharge associated with oddly-shaped precipitation and cloud particles leads to a reduction in the breakdown field intensity in moist air compared to dry air, but it is still well above most observations).
So, this leaves a couple possibilities. First, the atmosphere may, through macroscale charge seperation, reach breakdown field intensities, but those areas just haven't been sampled. In other words, the balloons / observations may have missed the highest E-field areas, meaning that there are "pockets" that have electric field intensities beyond that of the breakdown intensity. This is a possibility, but the vast majority of observations have recorded E-field intensities several times smaller than that required for breakdown (so it isn't like the observations are just a little weaker than is required for dielectric breakdown).
A second mechanism, mentioned previously, involves cosmic rays that result in RREA. We know, from surface observations, that the Earth is constantly being bombarded by extremely high-energy electrons (and other elementary particles). The theory goes that these high energy particles collide with atmospheric molecules/atoms at such energy that electrons are "shot off" the atmospheric atoms, which then collide with other atoms and molecules, knocking off more electrons (this is the so called electron shower, IIRC, and it's also where many more types elementary particles get involved, such as muons and tau leptons). Although this process may not directly initiate lightning (afterall, it would imply that we should frequently see lightning well away from storms), it is quite possible that RREA locally augments the electric field to the point of breakdown. One interesting piece of evidence that supports this possible mechanism is the observation of Bremsstrahlung X-rays in and near thunderstorms. These types of x-rays are the result of extremely rapid accelerations in high-energy particles (e.g. high-energy electrons rapidly changing directions), a possibility that fits very well with the cosmic ray / RREA theory.
Once initiation occurs, there are considerably fewer questions about the lightning process, though we still don't really know why some CGs are extremely branched / tortuous while others are relatively straight (dart-like), or why some strikes contain numerous return strokes while some only have one or two return strokes (i.e. some "pulse" numerous times while some don't). In addition, there's considerably question as to why some storms exhibit inverted polarity structure. In this regard, across the country, one of the most common areas for these inverted polarity storms is the high Plains (i.e. the high Plains sees a much higher-than-"normal" proportion of inverted polarity than the vast majority of the rest of the CONUS for reasons that are not clear attm).
By no means am I an expert in this, but that's my understanding of the initiation question.