Not very. If it ignores the base directory without direction, that could be bad. Imagine loading the MediaVPs without FS2. Ouch.
BUT, that doesn't mean that a setting or "TC" flag couldn't be set to define that behaviour. So, instead of a -tbp or -wcsaga flag, we just have a -TC flag (similar to -standalone) that does do that behaviour.
How would this new flag work? Force the engine to ignore the base dirs (data, vp)? The problem is this doesn't really solve the problem that started this entire thread of discussion, forcing flags, instead of -tbp or -wcsaga flags the mod would have to force the -TC flag.
It shouldn't be too hard to avoid the multiple directories thing if FS2 were to be shifted into being a mod itself. This of course sounds like a massive support headache.
If I had a pound for every time I wished we'd been able to do that..... 
But yes, telling people that they'd have to move their existing FS2 folder in order to install FS2_Open is just asking for trouble.
Agreed.
If we were to move the default fs2 data out of the engines main directory (or force the engine to ignore the main directory unless told to use it (which is what I think Zacam is getting at)), we would still have to have the engine start with certain flags so that it could find the game data to run. Unfortunately, the game engine is not omniscience, it cannot read the users mind as to which mod the user wants to load. Even the king of moddable engines (doom and half life) require the user to tell the engine were to find the game data. Doom and half life do this in engine, or with flags as kkmic stated earlier ( done as special shortcuts normally, you would be surprised at what is in the target box of some games short cuts).
Admittedly, the game engine could just start rooting around in it's game folder until it finds something, but this would require the TCs are installed in there own completely separate folders, which is not necessarily a problem, but seems to be different than how everything has worked in the past for this engine. Because it is so different from how it works now, I am sure that The_E would love us.

Can you be a bit more specific on the last part of the quote above? What would you like to see changed?
Have we looked at how other games handle this (benchmarked against our own needs, of course)?
What about users who just want to double click and go? (I mean anyone who can't handle the OpenAL installer is unlikely to want to be presented with a faceful of game information)
So far nothing that this launcher is asking of the user is any different than what the current launcher for windows is asking of the user, they just in a different place. The only differences are the installer/updater and the profiles, both of which are requested features and something that a user can just ignore. As noted by kkmic in the original post, there will be a default profile and the launcher will by default save any changes there, so this launcher will not need to be used any differently than the current one.
As for users that want to double click and go, the launcher is going to have sensible defaults, and if we can get it to work, the launcher choose sensible default flags for the user (like resolution, graphics and memory options). Because we are intending this launcher to be pointed to an existing freespace installation it will also support reading the current launcher's .ini. At that if the user wants to play the same mod that they played last time, they just start the launcher and click play, which is exactly the same as the current launcher. This is also why I mentioned in my last reply that the network stuff will be done after the launcher is ready to go so that this launcher even though it can do more things, will not be any slower than the current launcher is at load.