Its to be expected that *very very bad equiped agent* > *very very well equiped engineer* when it comes to aimed shot damage.
Its of course very stable and does craploads of damage 99% of the time. Its the reason i use it. But if you have it as only reliable way of doing damage, still far far away to even compare with full melee alpha. You wont kill anyone of the same level with just aimed shots each 11 seconds.
One can of course argue if its better to have one big punch each 11 seconds, or 99% kill chance each 1.5 a minute. If you are into title farming, propably the first one, if you are into sweet juicy kills, propably the second.
Of course if you consider only Battlestation, scale factor comes into game. Everyone has AS. Everyone has a root graft. You can say it melee disadvantage, and to some extent it of course is. But again, no one shouldnt survive encounter with 3-4 people, even if they all click only "o" button. But there are melee players that do survive, alpha someone , and can safely get away.
If you check city pvp, you'll see nothing has changed after LE, if you dont count everyone dying faster. There isnt any ranged domination, there isnt any AS domination, you have Agents, Reaver proffesions and melee Advies right on the top where you left them pre-LE. Any issue with battlestation pvp is a scale issue.