Sometimes it's better to go to a quiet world with your crew when looking for flagships. You don't have to compete with others for that ship. The EITC flagships I find are usually around Padres, but they are higher level.
I have noticed from the ships I've boarded the last few days, that the Navy ships have lower level crew and the EITC has the higher level crew. But again, that's just my experience and may not be others.
I do hope they make some more changes to this boarding process. The changes they did make on the 12th really kinda stinks