MediaBrowser can handle multiples the same way with the new server release as PLEX and these solutions are great but MB3 still has an advantage IMO in how it organizes libraries.
With MB you can create a user profile for "mobile" and another user profile for "HTPC" Let's just assume we name each user profile that for simplicity. Let's also assume you have an "admin" user profile too. You set up the mobile user profile to only show the mobile versions or whatver libraries you want included. You then set the HTPC user profile to only show the high quality stuff and not the libraries for mobile. Then your main admin user account shows everthing. That way on your phone you only browse the media optimized for mobile- if you really wanted to play something from one of the other libraries you just swap over to the admin account. But as a default only the libraries you want to show would so you don't have to worry about duplicates, or which file version you want to play- or have to take the time to decide and click that.
Same on the HTPC. You don't have to worry about accidentally playing the lower quality version or put any extra effort into double checking, or making a choice which version to play. If you are only browsing the full quality libraries you have no duplicates and no worries.
Either machine can swap over to the admin account and see them all if for some reason you wanted that too. It's two clicks and 2 seconds to change a profile.
MB server really is more advanced than PLEX in these areas. There is just a ton more set up options and you can even customize them for different people. For instance, my wife doesn't like horror movies so her profile I don't show those. I don't like trashy reality TV and my wife does so I don't show her TV shows in my profile. MB server also handle the traditional folder structure and nested folders and collections and box sets. So organizationally things are a lot neater while browsing your library. I have sub sections for certain things with a top level menu to enter them and this really can clean up a big library. Example: I have like 40 football movies because I am a football fan but I don't need all 40 showing in my movies library so I have folder with custom art that says "football movies" and inside it has all the football movies I have (Rudy, Any given Sunday, etc... etc.. ) So the effect is I can enter a mini football movie section from the main library but if I am not in the mood to watch something like that I only pass by a single movie folder for that category instead of passing by 40 movies.
It might sound silly but with a big library this is really a nice feature. Big box sets or certain types of movies can easily be categorized together. The box set plugins for MB3 do it automatically actually. You don't even have to move movies around or do it yourself. Just dump everything into a single folder lazy man style and the plug in will automatically create and group box sets. So for those different than me that do not want to take the time to really fine tune the presentation they can rely on the box set plugin to do all the heavy lifting so they can get a lot of the same benefits without any effort. MB3 wins either way in this area depending what type of person you are.
Plex doesn't handle nested folders and collections well.
Another area that is somewhat related is how MB3 handles grouping. MB3 totally kicks PLEX ass at this too. I can have a bunch of libraries and they get combined together or they don't and it's all handled at the top level library as a key set up feature of MB3. For example let's say I have a few movie categories: BLURAY RIPS, HD MOVIES, DVD MOVIES. I can go into any of those media libraries and see only those so if I go into the BLUERAY RIPS library I know every movie I am looking at is a BR rip. But I can also click on "movies" instead of navigating directly into the BR rips folder and in this case MB3 shows me all my movies. It will group DVD rips with BR rips and also group HD movies. So now when I click "movies" I am browsing every movie in my library. But if I want to only group certain movies I can do that too. And again you can customize what shows up on each user profile too. PLEX sucks at this. The PLEX server is mostly ignorant.
PLEX is great because it works. It's simplicity is appreciated by a lot of folks. But as soon as you try to fine tune your experience or improve and optimize it you realize MB3 just craps right in PLEX's mouth. It's no contest at all. Depending on what kind of experience you want and the things you value someone might find more value in one or the other. Both are great and have their strong points. But MB3 has advanced to the point it's beyond plex in it's abilities and most of that is due to the differences between PLEX server and MB3 server. MB3 server is really very powerful. There is also a focus right now on making it simple and keeping it simple. I think they are doing a good job walking that tightrope. Everyone loves advanced features and functionality, but no one wants a complicated set up process or hassle setting it up and using it. One of the things I really appreciate is how MB3 approaches this. Since I run the beta or developer builds I see the new features hit - but it's really refreshing to see how they get tweaked and improved and made easier to use and more simple in subsequent releases before it hit's official release. MB team constantly tries to tweak features to make them easier to use and the result is over time the project has really improved. Even from the start of this thread to today things are a lot different (better).