This game has and has had many other issues. Right now one of the biggest issues seems to be that new players are receiving the dreaded, "Your Mesh Files Differ from the Game Host" message. Almost every night I log on I can find someone who is complaining about that.
Another problem is Impulse. Presumably there are still people out there purchasing copies of the original Sins who can't understand why the 1.05 patch they downloaded from File Storage Site will not allow them to play online.
Another problem is overall player counts--from the very start this game had low online player counts. When a game peaks at having only 280 people online just two months after its release, it's a very bad sign of things to come. It also suggests that in the future the game is going to have a difficult time retaining the bare minimum critical mass of players needed to really sustain online multiplayer activity.
Another problem that helped contribute to the low early player counts was the inability of 80% of the players to be able to host their own games. Minidumps and desyncs did not help matters much either. <Edit> Back in those days, if the game host quit the game or surrendered (or minidumped)--if the game host lost--it would end the game for everyone. The Network window would pop up and it would say "Migrating" but the games would never migrate. (I had forgotten about all of that until I read Greyfox's next post.)
This game was also plagued by a perception amongst many players that it could not possibly be played online because their 10 player FFA games against the AI on the Huge Random Multistar map took 20 hours to play, and who in their right minds would want to play a smaller map such as the Huge Random Single Star map or a smaller map with fewer players such as the Large Random Single Star.
Then the buttons are mislabeled. The Multiplayer button is for LAN games and leads to a dead-end (unless you're going to direct connect to a friend's IP). Many people probably clicked the Ironclad Online button and couldn't figure out what it was for, then clickd the Multiplayer button and concluded that the game supported LAN play only. (Remember, a large percentage of all Sins purchasers have probably never been to the Sins website and might even be playing v1.00 or 1.05.)
To top it off, this game may have appealed to purchasers who are just predisposed to playing single player and might not have appealed to the kinds of people who play online multiplayer. It could be argued that it is even the birth of a new genre (4X-RTS) and that thus there isn't a base of people who play online multiplayer in other games to really even appeal to. (They might regard it as a nursery school-paced hack of an RTS.)
So, you see, a great many other issues and problems have contributed to Sins's low online player counts. It could also be argued that if this game had the online player counts it deserves, say 300 people online at any one time, that smurfing, at least in pro games, could be eliminated by requiring players to have accounts with 100+ wins on them to play in pugs and it wouldn't be hard to actually fill those games. Friends would still smurf newer players, but not as often because they would have 4v4's and 5v5 pro games to play instead. Furthermore, if this game had an active online multiplayer community that could generate buzz on gamer forums and elsewhere, it might lead to increased sales to people who play RTS games online, perhaps resulting in a constant influx of new players, decreasing the percentage of pros who smurf relative to the overall player population.
I do agree that this game could use some sort of a CD-key based player ranking system. For example, in Savage 2 (a free to download and play melee-style FPS with some RTS elements) every player has a "Skill Factor" rating.