Well the mini-series and 1st Season DVDs are the same as the original release in content. There are 16 discs because Season 3 is just 5 discs. There's no bonus content for series 3 it seems. I assume originally there was a bonus disc, but to save on packaging and costs, it's been omitted.
Incorrect. Season One has 4 discs, not 3. The reason this collection comes to 16 discs instead of 17 is because the 'bonus disc' for Season Three is missing. However, the only thing this 'bonus disc' contains in the individual set, is "Battlestar Galactica: The Story So Far" - a 43-minute special program that was aired on the Sci Fi Channel several times before the season three premiere, summarizing the previous two seasons and the miniseries, to try and get people who'd missed them interested in watching season three.
But that is fine, because this feature is entirely irrelevant for anyone who has seen the miniseries and first two seasons, hence the makers felt no need to include it in this complete box set - just the one for season three only, in case some people who buy it have not seen any previous seasons.
All the footage in "The Story So Far" is clips from the miniseries (for roughly the first 20 minutes), season one (roughly the next 10 minutes), and season two (the remaining 10 minutes). The only original material is the narration, by Mary McDonnell in her character of Laura Roslin - and no new information is imparted in this narration that the viewer would not have picked up anyway from watching the miniseries and the first two seasons (indeed, to fit everything into 43 minutes, several major story arcs are left out of "The Story So Far" - such as Helo getting marooned on Caprica, the arrival of the Battleship Pegasus, and the military coup that temporarily splits the fleet).
Buying the Complete Seasons 1-3 in this handy £40 set is far preferable to buying everything individually for £75. Apart from the missing 'Story So Far' disc, you'll get everything you would from buying the sets individually: the audio commentaries for the second season, the 'making of' feature for the miniseries, etc. A real bargain for an excellent series.