This is a question we've talked about previously amongst the team. It is actually a rather big problem (It was the main reason to do a single big release rather than multiple episodic releases). If you look at TBP you'll soon see the problems associated with doing multiple releases (Which eventually led to them making a final release and saying that it wouldn't be updated any further).
The way I see it, we have several options.
1) Release a single monolithic download for each release containing all of the new stuff along with all of the previous releases.
Advantages: Support is easy. We can easily check the version number to know exactly what files people are playing with.
Disadvantages: Ridiculously large bandwidth usage. By the time R4 comes out the game could easily be a gigabyte or more in size. Forcing people to download something that size is going to have an effect on the number of people who can play and is especially stupid if only a percentage of the download is actually new while the rest is the interface, ships and voice for R1 to 3, etc that the user may already have.
2) Separate "Patch" releases for R1.
Advantages: Much smaller downloads.
Disadvantages: Can easily become support hell. By R4 users will need to separately download R1 to R4 and install them (in the correct order) in order to have all the files they need in order to play the game. That's very annoying for the end user but more importantly increases the risk that someone will miss one of the downloads out. Furthermore later releases can very easily break missions from earlier release (especially 3rd party ones since the team won't be responsible for making sure that they work in the new release),
3) Online installer
Advantages: Can make things a lot easier for the end user
Disadvantages: Not everyone downloads on the same machine that they play on.
4) Completely separate releases
Advantages: No danger of later releases screwing up earlier ones
Disadvantages: No danger of later releases fixing problems with earlier ones either. If we keep R1 and R2 as completely separate games that would mean that any problems with R1 are still around being reported 2-3 years later, long after Diaspora or the SCP has fixed the issue. In addition you get 3rd party support hell with people installing R1 based campaigns on R4 and then wondering why they don't work.
5) Multiple release methods.
Advantages: Users can pick which download method suits them
Disadvantages: Makes support harder (different users will have different configurations). The more options you have the larger the chance that you'll stuff one of them up completely. Doesn't actually solve the disadvantages of the other methods so much as make the team have to deal with all of them.
Anyway that's what comes to mind so far. This isn't really going to be a huge issue for R1 so we can make the final decision when R2 is being worked on.
