There are some problems with the gameplay as I mentioned earlier, controls I think but also the save system (I believe you can only save between missions and there are no check points), it also has some problems with running properly from what I read in some people's opinion pieces.
It is also a bit half assed in design, apparently some parts were never properly finished or rushed. hence why there was some mod project to finish some of the problems.
BC mods, well they can update models and replace textures, they can add new systems, ships, and weapons. There is however no story based mods or campaigns, probably because it is quite difficult to make something like that for Bridge Commander (there is not a SDK for it so you would have to understand script writing among other things).
A bit of a shame really, I hope Excalibur works out well and that it can be made mod friendly for single player projects.
BTW, I really warn you with putting Kobiyashi Maru on Bridge Commander before you finish the campaign.
It balances the ships to the standards in the shows but as a result some hostiles become a lot more stronger and can for example quicker destroy targets you are suppose to protect.