If the mods are one click install, i'm definitely gonna go with that, but I am just a little worried about conflicting mods, will there be a warning or an easy to read description regarding any compatibility issues between mods?

I personally think that for more complex and conflicting mods Wrye Smash can never be replaced...

Nobody knows yet how it'll work and how one prioritizes conflicting mods

It's a good and interesting question! Especially since it's not one-click-install, but one-click-subscribe.
If you could install it, then you'd have at least some control.

Edit:
And as said, you'll probably still need decent mod manager

Skyrim Steamworks mods will work the same as other Steamworks-based content. You "subscribe" and it will auto-download the next time you launch the game. As modders upload updates to mods you already have installed, Steamworks will automatically download these updates.

Unless Bethesda corrects me, mod collisions (conflicts) will remain the problem of both modders and users, as it has always been for every TES title. Steamworks does not have any collision-detection built-in, so you'll still need to rely on modders to provide you with the information you need to make informed decisions about what mods you install. It's just like it was for Oblivion and Morrowind.

From what I could tell from the CK trailer, mods via Steamworks will be downloaded as an .esp and (optionally) an archive (probably .bsa) of assets. So once we have all our mods we'll be able to mash, bash and prioritise them using the tools developed by modders (many thanks to them ).

One point to bear in mind - almost certainly no .dll's or other executable code will be permitted in mods via Steamworks, so any mod that uses SKSE plugins (or, probably, ScriptDragon plugins) will have to be downloaded from elsewhere.

I'm also wondering if it would be easy to repackage mods to which you're subscribed.
So say there's a texture mod which you'd want 'on top' over other texture mods that conflict, that one can manually reinstall the mod after other mods are installed.

Will subscribed mods come in subfolders such as mods are now or will they just be a .bsa and an .esp?

You should be able to take raw files out of the Data folder just like in previous games. Steamworks is just a distribution system, but it doesn't do DRM or is required to use files on other computers that don't use Steamworks. I don't think reinstalling will be an option BUT, just manually move texture files you want out of the directory and then copy them back in after the conflicting mod is installed.

Subfolders, that is up to Bethesda. Probably won't know until they release it.

Why can't I quote posts ?

Anyway, "Subfolders, that is up to Bethesda. Probably won't know until they release it." True, but one of the options in the CK trailer was something like "Create archive and plugin and submit to Steamworks".

[edit]
Ah, the option was "Upload plugin and archive to Steam", with a separate "Create archive" option. So we'd probably have to use .bsa unpackers to extract files and folder structure from the archive.

Pretty sure you will get a prompt asking you if you want to overwrite files. If you click yes, it will overwrite them; no, it will roll back changes. Pretty straightforward stuff.

So, say mods will be released in their own .bsa and .esp (which I think might be the case), then I wonder in the case of conflicting things (eg textures) how Skyrim chooses one.
In the case of an unpacked mod it are those files (with archiveinvalidated) the take precedence. If there are multiple mods, it's the last installed mod (because of overwritten files).

Just very curious how it will play out.

I'm wondering what hoops you're going to have to jump through to download a mod without installing. I'm sure I'll be getting most of my mods from the Nexus, and Steam's subscription system looks like it might circumvent mod managers, so I'd rather download it's mods and install manually. In the trailer though I only see a "subscribe" button. So does that mean we have to subscribe, package the mod's files ourselves once its downloaded, then unsubscribe to prevent future overwrites? I hope they're not intentionally trying to make Steam Workshop everyone's one stop shop for mods by making it incompatible with other download sites, especially if their big surprise is a high res texture pack (that everybody will obviously want) available only through Steam.

Hopefully the steam workshop will give us the option to download files to a seperate folder. That would let us keep using mod managers without any conflicts. It would be nice if it just put all the mods in a seperate folder similiar to Wrye Bash's "Installers" folder and let users decide which of the downloaded mods they want to use at any given time.

I doubt Steam Workshop will be as fully featured as Wrye Bash though. It probably won't be able to keep track of multiple mods overriding the same file. That would be a really nice feature, especially considering the large number of texture replacers that are already available.

I think so, although I don't think you'll have to unsubscribe perse.
As long as you don't use the launcher, the mods won't be downloaded/updated.

I don't think they're trying to 'circumvent' anything - they're just providing the most straightforward way for total mod-using newbies to get mods without having to worry too much about issues like load-order or compatibility. I suspect that, as with their own DLC, every archive of assets will have to come with an .esp to say how those assets are used, and priority will be based on modified date of the .esp. If (IF) that were the case it would be, unfortunately, very unfriendly to things like large-scale texture replacers. But far more friendly to things like new weapons, NPCs or quests.

For more complex mods, needing code injection or large-scale file replacement, there are other sites to upload to. Those with the ambition to find the more complex mods will track them down easily enough, those who are satisfied with using a handful of simple mods without hassle will likely gravitate to Steam Workshop. Different sources for people with different wants, and (hopefully) everyone's happy.

Hmmm.. I forgot that the mods will be packaged in BSA files.. That'll make it hard to detect conflicts..

I do like the idea of Steam Workshop being as simple as possible, it's going to be introducing a lot of new people to mods, which is a good thing. More mod users means Bethesda will have more incentive to keep releasing developer kits for their games (plus having a bigger audience is nice.)

I guess .esp and .esm mods shouldn't cause any issues, load order managers will still work fine. Automatic installation of mods with loose files though would cause some serious headaches for NMM/WB's attempts at keeping track of overlapping files. If the CK wraps everything up in .bsa's though it could be OK, but I'm not familiar enough with .bsa's to know how overlapping .bsa archives would behave. It just worries me that they don't seem to be including a "download" button for more advanced users, it seems like it would be a no-brainer. I'm sure they're familiar enough with the modding process to know it would be useful (almost indispensable for anyone trying to use other sites along with the Workshop.)

This was Steam's idea, guaranteed. They've got to find more ways to box people into their system, dontcha know?

I'd be surprised if Bethesda haven't been in contact with both the Wrye and BOSS people on getting at least some of their stuff integrated in to the Steam Workshop/launcher stuff. More than surprised, I'd be disappointed. Especially considering I know at least one of them is in the beta.

Well, seen the lack of control over even simple things as mod order I doubt that, although it would be very neat of them to have some of that 'fancy' stuff built in.
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The only other way I can think of to ensure 100% compatibility, if they havent got compatibility-fixes built-in, is if the files (either in a bsa or subfolder) are 'marked' and when you want to subscribe to a mod that affects the same files as a mod you already are subscribed to it'd give off an error message or something ("unable to subscribe, you're already subscribed to a mod which edits the same files" or something).
(But if they'd have something as elaborate as that they might as well built it in )

The "download" buttons for more advanced mods are SkyrimNexus, SkyrimForge, TES Alliance and the like. Yes, it would have been nice if Steam Workshop had a facility to re-direct 'advanced mod users' to recommended sites - but that might have looked a little too much like an endorsemant of those sites by a commercial behemoth, trying to squeeze out the 'little guys'. You can bet that there'd be people saying "Oh, those sites paid Bethesda for a mention, guaranteed."

A couple of quotes from Ashley Cheng

Maybe he's a liar - I personally doubt it. I think their intentions are to do a good job for the majority of their customers (most of whom have never used a mod). Of course they can't please everybody and still keep things simple, so if you want complete control of your mods you just don't use Steam Workshop - simple as that.

You guess wrong. You could have a landscape altering mod that only used vanilla assets and therefore consisted only of an esm or and esp. Have two that alter the same cells, as happened frequently with Oblivion where, for example, you got a house mod and a Unique Landscapes mod in the same area and whoops! Land tears and all sorts of nasties. That's why Nexus has a series of compatibility patches for the UL mods up there.

I hope the Wrye Bash and BOSS teams are still going to make versions that do not require you to use Steam Workshop if you don't plan to.

You mean, like the existing versions ?

Look, absolute worst-case scenario - you use a .bsa unpacker to unpack a Skyrim Workshop mod to a directory. You unsubscibe from the mod. You use whatever mod-manager you prefer to re-pack the extracted directory to that manager's format. You re-instal it. You Bash, Mash and BOSS away to your heart's content. A few extra steps, which are only needed if the modder doesn't upload it anywhere else.

I don't anticipate that ever changing. Wrye Bash and BOSS both exist outside of the Workshop already. I can't see why you'd even think there would be changes made to either utility to only work with the Workshop and nothing else.

So how are you are supposed to put simple mods from the steam workshop under control of Bash? Because installs controlled by two different mod managers at once is a broken install waiting to happen.

Does that mean there will be some Wrye or BOSS integration with SW?