An experimental patch has been developed that extends taskforces from a maximum of 9 ships to 18 ships.
You can get it here:
BotF Taskforces Patch at sourceforge
This patch has been under development on-and-off since 2011, but was too unstable for use. With contributions from thunderchero, it now seems quite stable, but the patch needs further testing.
There are some caveats to using this patch:

It breaks compatibility with existing SAV files! You can't load up your old savegames, nor can new savegames be loaded up with an unpatched version.

All participants in a multiplayer game must patch the game with the same ships per taskforce limit (e.g. all players with 18 ships).

As a workaround for an instability in the patch, the AI has been prevented for forming taskforces (i.e. the AI has only 1 ship per taskforce).
Other notes:

Because of the complexity of this patch, it does conflict with other patches such as the Instant Terraforming bugfix and the Ship Scrapping exploit fix.
Therefore the taskforce patchtool will check for these patches, and automatically adjust them. So if you want those patches, install them first, then the taskforces patch!

Finally, if you are modder,
make a backup of your trek.exe. The patch has no uninstall option right now.