The problem Airbus had o the A380 was trying to make CATIA V4 and CATIA V5 work together, something that you get told at the beginning of any CATIA conversion course will not work. Why Airbus thought it could ignore this, I'm not sure, probably money is at the root of it (couldn't afford to upgrade all the software and workstations at the same time). Competition is very much still about, directly in the form of UG NX and also a variety of other CAD packages depending on cost (UG and CATIA are thousands of pounds a seat, cheap compared to upwards of £40K+ for an Finite Element Analysis licence).
IGES, STEP, et al. exist but sending data means the part creation history gets lost. CATIA and UG NX native files are parametric, so by tweaking a dimension the rest of the model (and any drawings based on it) automatically update. Using IGES, etc loses this data, leaving a 'dumb' solid and the result is not always very good anyway.
The slippages for Airbus and Boeing are just reminding everybody that jet airliners are complex and getting more so. The airworthiness rules keep raising the bar (as they should, as more and more understanding of the causes of aircraft crashes get fed back into each new revision). The time that has lapsed since the last major aircraft designs will definitely not have helped (B777 and A330/340 in the mid '90s). The experienced people changing jobs/company, managers who have never had to project manage something this big before, etc.
As for lightning protection there will be a copper mesh incorporated into the composite layup of the panels and this will provide the faraday cage effect required. All the various layups and design configurations would have to undergo lightning strike testing (and obviously pass!) to achieve airworthiness certification.
The approach is well known, for example, the engine nacelles on a variety of jet aircraft (Airbus, Boeing, Bombardier, Embraer, etc) have been manufactured in this way for more than a decade.