Over the last two or three days, I had to bypass the launcher by opening GameClient under {Steam Installation}/steamapps/common/Star Trek Online/Star Trek Online/Live/ although that didn't work well either, as I could not access the account or login server. Part of it appeared to be due to the Level 3 blackout, although there were those posts out there (on the STO and Neverwinter forums) that seemed to contradict the idea that this was the full cause of the disruption in service. There were also things said about Comcast customers being the main users who had trouble with the lag, rubber-banding, SNR's, disconnections, and downright not even being able to get past (or to) the character selection screen.
I'm relieved to say that, at least where I'm at, this problem has gone away, at least for the moment. But there was at least a 24 hour period there where I could not open the launcher, at all, nor could I try and bypass it for any better results. This kind of thing happens quite often these days, but in my experience at least, it hasn't lasted quite as long as this. Once the problem 'seemed' to go away, there wasn't even an ounce of lag in game for me, and I played for about three hours. Keep in mind that this is the exception and not the rule.
In at least this most recent case of lag and SNRs and such, it doesn't appear to be Cryptic/PWE exclusively. Though there are still lag issues with the command specialization tree, much of what's going on might sometimes be better attributed to that old adage, $4!$ happens. In this case, it appears that some of it may have been the Level 3 blackout, some may have been Comcast, and some could have been ... well, who knows. Cryptic has been hard at work (sleep? j/k) attempting to clear up some of the ability-associated lag, although that seems to have had undesired effects with each patch. I use the word 'seems' a lot, as I don't know for sure what's going on. I'd expect a few more ability-related lag fixes in the next few patches, along with some graphics-related fixes that are currently on the Tribble server.
I was relieved that the problem had, at least temporarily, gone away as the game is somewhat about Star Trek, and I know some people who play it a bit. The grinding, lag, and other parts that aren't quite so appealing I try to punch through and make the best of, but this last bit of lag and no server responses whatsoever have been a wee bit frustrating.