MMO's are dynamic. As such there's always going to be some inconvenience as developers struggle to keep the content fresh and engaging. Still, there are ways to minimize the pain that Star Trek Online doesn't seem to have discovered yet.
The Gray Area:
I don't know of any game released in the past 5 years that hasn't needed at least one major update. It's usually a relatively painless process and if it comes from a source like Steam you may never have to worry about it. Distribution channels like Steam and Origin usually roll the updates into their installation routines so that a fresh install doesn't have you spending half the night waiting for downloads to complete before you ever see the title screen.
I came to know Star Trek Online via Steam and installed the game using it's mechanisms. Star Trek Online installation files compress into 4GB and expand to 10GB on installation. Imagine my surprise when I restored the game from my installation backup only to find another 3.5GB of downloads waiting to be completed. The process was automatic but unexpectedly ate up an hour of my weekly Lan party.
Speaking of updates, Star Trek Online seems to update itself every time I log in to the game. That's good in the sense of keeping the game up to date with fresh content and bug fixes but it takes away from time in the game.
Updates aren't limited to just starting the game either. Most missions involve the download or update of mission content before the game will continue. At least the load screens are interesting. As large as the game installation is it appears that Cryptic does not provide the complete installation package but rather provides a basic structure then adds to it as needed. Since distribution is via online, It's likely that including the complete package would overwhelm most broadband connections and unnecessarily burden update servers by uploading files to clients that were not yet in use.
Since I've spent so much time on the start screen perhaps I should segue to the next minor annoyance, namely the login screen or rather getting to it.
Star Trek Online is a property that has changed ownership three times and has had two different developers since the project began in 2004. With that much turnover there's bound to be some bugs and they show up prominently in the confusing registration process. In my experience I wasn't sure if I was registered with the developer, Cryptic or the Publisher, Perfect World Entertainment. I still don't know which one I signed up with but at least I can get in the game.
This is a free to play MMO which means you don't have to invest anything but time and hard drive space to enjoy the game. You can purchase a subscription and upgrade your experience or make a one-time purchase of individual upgrade packages. The problem is that both the publisher and the developer offer upgrades both in-game and outside of the game. Both use different currencies with a confusing exchange rate that rivals any Forex chart. Here's a suggestion; either standardize on an in-game currency or get rid of it entirely. Such ambiguity just confuses potential customers and a confused customer is rarely a paying customer.
So there it is. Everything I know about Star Trek Online. With 55 hours into the game there's definitely something I like about it. What I'm not sure of is whether its attributable to the game itself or just my desire to have a decent Star Trek title to play again. The game has issues but patches are a daily occurrence and nothing I've citied above has caused me to completely give up on the game. The partnership with Steam was an excellent distribution move as was the change from purely subscription based to Free to play.
In the end the game is free and thus far has given me a lot more enjoyment than some recent titles that I actually paid for. If I continue to enjoy the game then at some point I'll likely purchase an upgrade package if for no other reason to show support for it.
What's nice about this game is that the penalty for not putting skin into the game is little more than an inconvenience. In many free to play games with paid options, players who purchase upgrades are often able to unfairly dominate other players. Star Trek Online thus far doesn't seem to follow that model. Purchasing a subscription may get you a better ship or help you advance your Starfleet career but it won't allow you to bully anyone because of it.
It's an MMO with a focus on more personal experience.