It's funny that you mention the non-skirmish missions as the filler ones. Most people who like RTS's utterly loathe the lack of a skirmish focus in most single-player campaigns. Build-destroy maps are the only ones that can offer up anything approaching a challenge, by making you face a superior force without any built-in 'auto-win' strategy. Non build-destroy maps are retarded in an RTS because they take the tactical aspect out of it. Instead of having a variety of strategies open to you, while requiring you to scout and counter your opponent's strategies, you're forced into adopting the one (usually painfully obvious) 'correct' strategy for winning that map. It's like saying 'AI is so shite compared to a real human opponent on skirmish maps, that we're better off making it REALLY retarded so that it only adopts the one preset build order, unit combination and attack pattern'.
Shite like that is the reason why about 75% of WC3 players were so utterly unequipped and unprepared for playing online ranked matches when they finished the singler-player campain, that they became competely disenfranchised through their inability to understand why they were getting their ass kicked (omg, there must be some singular auto-win unit combination! I know I'll look it up on the net - whoah here's some build orders, but there's a lot of stuff about scouting, map control and responding to opponents that I don't understand, but it must be the magic unit combo that's important...WWAAAAGHH!! I keep losing even though I used the magic unit combo! This game must be rigged!) and gave up, playing nothing but custom maps from then on. The focus on 'one-strategy' puzzle maps at the expense of skirmishes meant that the campaign did nothing to introduce new players to scouting, map control, recognising your opponent's strategy in advance (fast-teching orc with 2 beasteries? That means he's going mass wyverns/raiders and I won't have an effective counter until tier 3.5 - much too far away. I'd better either (a) cripple his economy before the tech finishes, (b) stop teching, build another crypt, sell unnecessary buildings and do an all-or-nothing rush, or (c) expand, keep engaging him away from my base, so I can build up an economic advantage to counter his military one and then beat him in tier 3), use hit-n-retreat tactics, or balancing when to tech vs expand vs rush vs harass - basically nothing except for 'build as many units as you can of the highest tech tier you can, and send them to your opponent's base.
Then they hit multiplayer where you can't just tech up at your leisure, and even if you do, all 'mass x top-end unit' have a cheaper counter.
And for what? A story, that is completely non-interactive and told entirely through cutscenes? It doesn't matter what set of 'badass' lore you want to invent to justify why the tier 1 melee unit for one race does 7 damage and has 3 armour, whilst the one for another race does 3 damage and has 7 armour - when the only ways that the lore will show up in the game will be (1) the unit graphs (and we haven't suddenly become graphics-whores have we?), and (2) the cutscenes. The single player storyline matters as much to RTSs as Werdna's backstory did in Wizardry 1 - skipping it entirely would not affect the gameplay one bit. Now that changed in RPGs because they started moving away from pure wargaming to having C+C and incorporating dialogue as a form of gameplay. RTSs, on the other hand, are still wargaming and so storyline is as irrelevant to gameplay as it always has been. Sure, they could introduce dialogue-driven C+C into RTS games, though that isn't describing any RTS made just yet (though the original designs for WC3 seem to have envisaged that). But when you consider that in RTSs the ratio of combat to dialogue AND C+C has to be enormous, otherwise you'd have an RTS in the same vein that FO3 was an RPG, it seems most unlikely that anyone would be moved enough by the plot to choose on any basis other than what will give the greatest practical gameplay advantage. Which, again, means that storyline would be still be irreelevant to the gameplay.
And take the storyline away from the puzzle maps and you've got a gimped skirmish map with all but one strategic option taken away.
