First introduced in Return of the Jedi, and embodied in the character of Admiral Akbar, the Mon Calamari race was greatly expanded upon in the RPG books and in the novels and comics. There was a bit of canonical turmoil between the RPG and the movies when prequels came out (yeah, the prequels tended to do that). In the RPG, Mon Calamari had only JUST been discovered and subjugated by the Empire. In the movies, it was shown that the Mon Cal had evidently been part of galactic society for some years (witness the Mon-Cal in senate scenes and at the aquatic ballet in Revenge of the Sith). In the first Clone Wars Cartoons, it was further shown that the Mon Calamari and the Quarren (who share this homeworld) actually battled against eachother during the Clone Wars—with the Mon Cal on the side of the Republic and the Quarren siding with the Separatists.
This is one of those cases where I like the movie version of the story better than the RPG. Considering their skill in building starships, it would seem to make sense that the Mon Cal had been doing that for some time prior to the rise of the Empire. It actually doesn't take that much to alter the RPG story to fit in any case.
Where the real problems arise (at least for me) is the status of the planet during the Rebellion era. In the game, it is said that the Mon Cal rose up against the Empire, destroying the garrison force and declaring openly their resistance. They then turned their shipyards to the task of building warships for the Rebel Fleet. This is all well and good, but...one would think that the Empire would want to put a stop to this. And yet, we are expected to believe that they allowed the planet to retain its freedom for perhaps as long as a couple years prior to the death of the Emperor and the collapse of his fleet.
In the game (as suggested in the sourcebooks and the adventure 'Death in the Undercity') we are told that the Mon Cal maintain a large garrison fleet in their home system—large enough to keep it safe from direct Imperial assault. This seems a contradiction to me, since it is also implied that even the main Rebel fleet cannot openly stand against the Empire. It is also suggested that the Empire, after the destruction of the first Death Star, is spread so thin that they can't pull together enough ships to take Mon Calamari out. Again, this seems implausible, since they are able to crush all opposition elsewhere. Considering the Mon Cal seemed to be the MAJOR supplier of the Rebel Fleet, one would think they could scrape up enough ships from elsewhere to stomp on the threat—even if they lost a few less strategically important systems to do it.
Therefore, we are left with only a couple explanations for this. First of all, maybe the Imperial fleet IS too spread out. It is said that in the post Death Star era the Imperials were increasingly hard-pressed to face the number of uprisings. Perhaps the empire was holding back a large portion of its fleet to counter the main Rebel Fleet (which could strike at any time). This is the weakest theory (in my opinion) as the Empire was always portrayed as 'all mighty'—and if it couldn't handle one major planetary insurrection, then something was wrong.
The second possibility is that the Empire just hadn't gotten around to stomping Mon Calamari yet. Maybe they didn't realize the strategic importance of it (difficult to believe) or maybe they felt it was too far out in the boonies to care about (again difficult to believe).
The third possibility is the more interesting one—perhaps the Emperor didn't WANT to destroy Mon Calamari for some unrevealed reason. It was quite evident that Palpatine was a very clever guy, always thinking several steps ahead of his opponents. Perhaps he was following the whole 'keep your friends close and your enemies closer' philosophy. Afterall, if he allowed Mon Calamari to maintain its freedom, he kept the Rebellion from hiding or spreading out its major shipyards. So when he finally DID crush Rebel high-command or the fleet, he could then move on to crush Calamari—since he knew right where to find them. Though interesting, I'm not certain this was the case or even if it would be a wise thing for the Emperor to do.
Ultimately, in my own campaign, I have (only recently) decided the reason that the Empire never crushed Mon Calamari was actually a combination of the above theories. The Empire WAS spread out. They WERE dismissive of the strategic importance of the system (afterall, the Mon Cal are 'only' Aliens). And the Emperor DID want to 'keep his enemies closer'. When you throw all three of these together, you get something that is much more believable (to me at least). But all things considered, Mon Calamari would be a tense planet during this time, knowing full well that they are operating on borrowed time—never knowing when the Imperial Hammer is finally going to drop.
Of course when I first pondered this whole situation it raised the question to me of why the Alliance didn't just base its high-command in this 'secure' system. But looking at the above, I think I've now answered my own question: It would have been putting all your eggs in one basket. With the shipyards AND high command all in one place, Mon Calamari would have become too important to ignore. Thus, by keeping the Alliance spread out—high command in one place, fleet in another—Mon Calamari was just one 'moderate' sized target instead of one huge bullseye.
There, now I feel better about the whole situation. Hope you do too.