This makes sense, really.
Unfortunately, the ludonarrative dissonance you mention is hard to fix without overhauling the entire campaign and adding advanced scripting capabilities to the engine. And if the designers did that, they’d have to decide what they consider more important: the story or the gameplay.
- If the gameplay is more important and you want to keep the sense of grand scale with sieges and naval combat, then keep all the base-building missions, but frame them in a story that makes sense. For example, the campaign could be about the immediate surroundings of the Dark Portal on both sides. If you wanted to keep the artifact heist, you could make the story about establishing a presence around the Dark Portal and defending it while the artifacts are being collected elsewhere, or perhaps repelling a human invasion through the Dark Portal. If advanced scripting was possible, you could make a “survive for X minutes” mission in the style of Starcraft and Warcraft 3, defending Ner’zhul from invading human armies while he opens the portals.
- If the story is more important, then a heist story should feel like one. Make most of the missions hero-centric, featuring infiltration and stealth. Even with the limited capabilities of the Warcraft 2 engine, I think there are ways to make the missions varied. They’ve already worked around the inability to place items on the maps by establishing in mission briefings that the items are held by particular units that you need to rescue or kill. You could, for example, make a mission about gathering four human traitors who can help you recover a MacGuffin, represented by peasant or mage units like in missions with Alterac, and the catch would be that they’re scattered across the map and your forces are very limited. Then the next mission briefing would establish that your human lackeys broke into a vault and retrieved the MacGuffin for you.
Make the story fit the gameplay, or make the gameplay fit the story. Either works.
The “Ner’zhul has read the script” problem is much much easier to fix and only requires some dialogue changes. Just establish that he got all the knowledge about the other artifacts by attuning to the Skull of Gul’dan, which you retrieve in the second mission of the campaign, — and that’s when he formulated the entire plan involving the artifact heist and the opening of the new portals. Bam, you have your campaign objective right away, you know where each artifact is, and the characters don’t have to rely on contrived super-senses to sniff them out.