Personally (this is totally subjective), I feel that SFC actually boosted SFB more than the other way around. I don't know if the Interplay/ADB contract stated the SFB material had to be included, but I bet it got ADB more than a few new customers or reintroduced old ones to the game. I have bought all the mainstream (alpha sector) SFB modules of the current ruleset from ADB's site. I don't even PLAY SFB anymore, and didn't have a ton of opportunities to do so in the '80s when I WAS playing. Those SFB products are a wealth of information for SFC mods -- I know that much, at least.
The discussions about D&D don't really sway me much either way; it was (and is?) arguably the most popular RPG ever, and would have eventually had a lot of successful computer games based on its basic ideas. I also don't buy the simplified ruleset comparison, since SFC was already using a certain level of depth. It's one thing to take a simpler game and make it more complex as the medium and players become better suited for it. It is quite another to simplify a solid game, requiring less of its players. Now, I don't feel that SFC3 was solely a simplification (some things like more gradual range/damage tables just make better sense when you're not tied to dice rolls), but it was certainly perceived as "dumbed down" by a percentage of its potential audience.
About the shows and such, I'd have to agree a well-written wartime Trek show would be a much bigger draw for me than Voyager or Enterprise have been. DS9, in my opinion, was absolutely the best Trek for about 2 years during the meat of the Dominion War story arc. Sure, there were diversions and filler stories, but what really made the show worthwhile was the almost Shakespearean politics and character tension that served to fuel the battle scenes that so many sci-fi fans enjoy. A similar treatment could be done with an SFB-based war story, though it would have to be far more limited in scope just to allow for proper character development. A Fed/Gorn/Kzinti vs. Klingon/Lyran/Romulan (sorry ISC and Hydrans) storyline would offer a great deal of potential. Not only would the two factions be going at each other, but there would also be a wealth of internal politics and intra-alliance squabbles to keep things interesting. I suppose this could be done in a post-Enterprise, pre-TOS time period with perhaps some modifications to or replacements for the Lyrans/Kzinti.
Of course, there will be many who point out "Gene" would never have accepted a war-torn universe for his ideal world. I don't think he was as divine as many people make him out to be. Specifically, I think it is hypocrisy to include mass destruction of life (how high were the death tolls of Trek episodes in ships and crew?) at the push of a button without also allowing for, and indeed examining closely, wars and their effects on the lives of the people caught in the middle of them. However, I have probably angered enough people already, so I won't take this discussion further.
Getting back to what I feel has been really valuable in this thread, I really do think OP is the best game of the series, if only that D2 were fixed. I know I've said it many times, but I think it bears repeating.