Another issue that Loki contended with was the fact that most of their games ran at a lower framerate than the Windows counterpart. Most serious gaming fans want to use their hardware to its maximum potential especially the FPS multi-player twitch gamers. Valve has a lot more leverage in this regard than Loki ever did. We all know (because they said so) they are working with the major GPU players to get better drivers made. But also, they don't just port games, they make them. The Source engine is very popular and they have already tweaked it significantly so not only is it competitive with how it runs on Windows but it actually surpasses it in maximum frames per second.
Another thing Loki dealt with was Linux users were a bit more idealistic in the 90's. We still held out hope that AAA game titles would just "appear" on Linux. Fast forward to the present day and I doubt many actually believe this. The problem back then was that if you expected Free top tier games to just appear you had less incentive to actually buy. I think Linux users are a bit more pragmatic now and are much more willing to pay for a proprietary binary as it's pretty clear that that's the only way you're going to play. So this is a psychological barrier Valve doesn't have to overcome anymore.
Basically, I think Valve is approaching this with the same methodical precision that Tesla is approaching the electric car space. Look at the problems that exist in an objective way and devise solutions one by one until you achieve success. Valve may still falter but it won't be for ignoring any lessons Loki could have provided.