Wrote a couple of pages of analysis, decided I was overdoing it, saved it off and starting over a bit more simply.
So, lets see if I have this right.
[1] Shadowfighters lose dogfights, because they are almost always severely outnumbered or outfought, or both.
[2] Shadowfighters survive normal fire a little better than most other elite fighters, though a little worse than cheap fighters and lose horribly to anti-fighter fire.
[3] Shadowfighters have straight firepower which is about as good as it gets, which makes them quite nasty and definetely up to par if they can avoid the above two problems.
[4] Shadow players have minimal choice at low PL's, leading to situations in which they will have to face problems [1] or [2] fairly often.
I think, increasing numbers per wing to 3 with no other changes, while the easiest change, runs a high risk of not significantly solving problems [1] and [2] and does nothing about [4], while it does notably effect [3], which effectively penalizes oponents who don't have good anti-fighter/fighter capabilities of there own.
Increasing the flights per wing to 3 whilst decreasing the AD from 3 to 2 (and keeping the specials) might help [1] and [2] whilst leaving [3] untouched and would be a very safe option, but still isn't getting to the heart of the problem.
Allowing shields to work vs anti-fighter fire would help [2] somewhat and I think combined with the above suggestion would get as close to solving the given problem as possible without significantly changing the character of the fighters as laid out by Mr Sprange above.
Though at the end of the day I can't help but think that [4] is the true problem and isn't one we can solve with changes to the fighters themselves - It seems to me what the shadows could use most would be simply another option somewhere, either at patrol or skirmish so they aren't forced to take either a horde of what are essentially bombers or a small number of raid level ships and thus easing the overall problem.