While the priority system works well for friendly or narrative games, that's because it functions as a 'loose' point system at the level you'd use for such games anyways - IE, 'bring something like 2000 points of fun, fluffy ships/troops/whatever' without worrying too much about exact point costs or min/maxing. If you're just playing a random game for fun, and using even 'underpowered' ships, then all you need is a basic guideline as to how powerful a ship is. It really does break down in a competitive selection setting though, and makes it much harder to 'fine tune' balance, not to mention restricting ship diversity by forcing them to either conform to one of a few specific power levels or be unbalanced one way or another. The command variants, for instance, are just unavoidably unworkable with the current PL system. They aren't going to be worth 2 of their unmodified brethren, nor can they be the same level or there would be no point in taking the regular type.
Someone (I think it was chern) mentioned the idea of ships having a "PL +" or "PL -", which is a reasonble half way option. Before I stopped doing anything game related for months, I was working on a sort of unofficial supplement with a bunch of hypothetical or Crusade-era ships (once I see Armageddon & get back into the game I might finish it, especially as all the ships there sound like they're huge, terrifying monsters, while my supplement was more based around new generations of smaller ships or just fresh designs. But I digress.) Since I was both unsure of my ability to balance things perfectly and I thought it gave more flexibility in designing, I was qualifying PLs with a "+", "++", "-" or "--" to give an impression of how powerful a ship was in comparison to others of that PL. I never came up with specific rules for limiting selection based on that, but it doesn't seem like it would be too hard for Mongoose to publish such rules and just slap on +s or -s to new ships or old ones via a download.
I'd as soon just see a points system, but that would be such a giant overhaul that it would be tough to just do via an online addendum. A + and - system seems workable without a whole new rulebook.