Capcom has come back with a statement:
In Resident Evil: The Mercenaries 3D, all mission progress is saved directly to the Nintendo 3DS cartridge, where it cannot be reset, a spokesman told Kotaku. The nature of the game invites high levels of replayability in order to improve mission scores. In addition, this feature does not remove any content available for users. Second-hand game sales were not a factor in this development decision, so we hope that all our consumers will be able to enjoy the entirety of the survival-action experiences that the game does offer.
Source:
http://www.kotaku.com.au/2011/06/capcom-denies-used-game-sales-had-anything-to-do-with-forever-saves/#commentsSo basically a blank statement that dodges the real question at hand. There's no explanation to why it can 'only save on the cartridge', just mentions that it does, without explaining the reasoning behind this, and the statement that it has nothing to do with used game sales is probably an outright lie.
I'll bet anything it was a test of the waters, to see what consumers are willing to put up with and whether they can get away with it in the future. It worked for pre-release DLC.
EB Games in Australia have said they will not accept any trade ins, and Japanese retailers have already said that they will only be offering 500 yen (approx $6 AUD) trade in value for the game because of this issue. Sounds like they've been successful in their plan.
This would be a major problem if the game was actually story based character progression game but for an arcade action experience like Mercenaries it shouldnt really bother anyone which is what capcom was probably thinking.
It doesn't seem that big a problem in a game like this, and indeed it probably doesn't affect the end game all that much - the problem is it establishes a precedent. If they get away with it here, you'll start seeing it creep into more and more games with more intrusive results. Again, just look at pre-release Download Content. Nowadays development teams are splitting the last fourth of a games content into planned DLC, which is often still located on the disc at release, you just pay a code to unlock it.
Even if you do buy all the DLC, what happens in 10 years time when you want to replay your old games and the server no longer exists, and Sony/Microsoft have moved on and no longer support it? Compound this by a million if you start up the game and it's already had everything completed.